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Brewer A, Sathe G, Pflug BE, Clarke RG, Macartney TJ, Sapkota GP. Mapping the substrate landscape of protein phosphatase 2A catalytic subunit PPP2CA. iScience 2024; 27:109302. [PMID: 38450154 PMCID: PMC10915630 DOI: 10.1016/j.isci.2024.109302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/18/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Protein phosphatase 2A (PP2A) is an essential Ser/Thr phosphatase. The PP2A holoenzyme complex comprises a scaffolding (A), regulatory (B), and catalytic (C) subunit, with PPP2CA being the principal catalytic subunit. The full scope of PP2A substrates in cells remains to be defined. To address this, we employed dTAG proteolysis-targeting chimeras to efficiently and selectively degrade dTAG-PPP2CA in homozygous knock-in HEK293 cells. Unbiased global phospho-proteomics identified 2,204 proteins with significantly increased phosphorylation upon dTAG-PPP2CA degradation, implicating them as potential PPP2CA substrates. A vast majority of these are novel. Bioinformatic analyses revealed involvement of the potential PPP2CA substrates in spliceosome function, cell cycle, RNA transport, and ubiquitin-mediated proteolysis. We identify a pSP/pTP motif as a predominant target for PPP2CA and confirm some of our phospho-proteomic data with immunoblotting. We provide an in-depth atlas of potential PPP2CA substrates and establish targeted degradation as a robust tool to unveil phosphatase substrates in cells.
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Affiliation(s)
- Abigail Brewer
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Gajanan Sathe
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Billie E. Pflug
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Rosemary G. Clarke
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Thomas J. Macartney
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Gopal P. Sapkota
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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2
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Bellad A, Rangiah K, Sathe G, Dey G, Appadorai PK, Lokanatha H, Murthy PR, Gowdra A, Pandey A. Identification of a rare [ G γ( A γδβ) 0 ] -thalassemia using tandem mass spectrometry. Proteomics 2024:e2300495. [PMID: 38212249 DOI: 10.1002/pmic.202300495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/23/2023] [Accepted: 01/03/2024] [Indexed: 01/13/2024]
Abstract
Thalassemias are a group of inherited monogenic disorders characterized by defects in the synthesis of one or more of the globin chain subunits of the hemoglobin tetramer. Delta-beta (δβ-) thalassemia has large deletions in the β globin gene cluster involving δ- and β-globin genes, leading to absent or reduced synthesis of both δ- and β-globin chains. Here, we used direct globin-chain analysis using tandem mass spectrometry for the diagnosis of δβ-thalassemia. Two cases from unrelated families were recruited for the study based on clinical and hematological evaluation. Peptides obtained after trypsin digestion of proteins extracted from red blood cell pellets from two affected individuals and their parents were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Mass spectrometric analysis revealed a severe reduction in δ, β, and Aγ globin proteins with increased G γ globin protein in the affected individuals. The diagnosis of G γ(A γδβ)0 -thalassemia in the homozygous state in the affected individuals and in the heterozygous state in the parents was made from our results. The diagnosis was confirmed at the genetic level using multiplex ligation-dependent probe amplification (MLPA). Our findings demonstrate the utility of direct globin protein quantitation using LC-MS/MS to quantify individual globin proteins reflecting changes in globin production. This approach can be utilized for accurate and timely diagnosis of hemoglobinopathies, including rare variants, where existing diagnostic methods provide inconclusive results.
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Affiliation(s)
- Anikha Bellad
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Kannan Rangiah
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | | | - Hemalatha Lokanatha
- Department of Pathology, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
| | - Pradeep Rudra Murthy
- Department of Pathology, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
| | - Aruna Gowdra
- Department of Biochemistry, Indira Gandhi Institute of Child Health, Bangalore, Karnataka, India
| | - Akhilesh Pandey
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
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3
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Sathe G, Sapkota GP. Proteomic approaches advancing targeted protein degradation. Trends Pharmacol Sci 2023; 44:786-801. [PMID: 37778939 DOI: 10.1016/j.tips.2023.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 10/03/2023]
Abstract
Targeted protein degradation (TPD) is an emerging modality for research and therapeutics. Most TPD approaches harness cellular ubiquitin-dependent proteolytic pathways. Proteolysis-targeting chimeras (PROTACs) and molecular glue (MG) degraders (MGDs) represent the most advanced TPD approaches, with some already used in clinical settings. Despite these advances, TPD still faces many challenges, pertaining to both the development of effective, selective, and tissue-penetrant degraders and understanding their mode of action. In this review, we focus on progress made in addressing these challenges. In particular, we discuss the utility and application of recent proteomic approaches as indispensable tools to enable insights into degrader development, including target engagement, degradation selectivity, efficacy, safety, and mode of action.
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Affiliation(s)
- Gajanan Sathe
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Gopal P Sapkota
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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4
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Gowthami N, Pursotham N, Dey G, Ghose V, Sathe G, Pruthi N, Shukla D, Gayathri N, Santhoshkumar R, Padmanabhan B, Chandramohan V, Mahadevan A, Srinivas Bharath MM. Neuroanatomical zones of human traumatic brain injury reveal significant differences in protein profile and protein oxidation: Implications for secondary injury events. J Neurochem 2023; 167:218-247. [PMID: 37694499 DOI: 10.1111/jnc.15953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023]
Abstract
Traumatic brain injury (TBI) causes significant neurological deficits and long-term degenerative changes. Primary injury in TBI entails distinct neuroanatomical zones, i.e., contusion (Ct) and pericontusion (PC). Their dynamic expansion could contribute to unpredictable neurological deterioration in patients. Molecular characterization of these zones compared with away from contusion (AC) zone is invaluable for TBI management. Using proteomics-based approach, we were able to distinguish Ct, PC and AC zones in human TBI brains. Ct was associated with structural changes (blood-brain barrier (BBB) disruption, neuroinflammation, axonal injury, demyelination and ferroptosis), while PC was associated with initial events of secondary injury (glutamate excitotoxicity, glial activation, accumulation of cytoskeleton proteins, oxidative stress, endocytosis) and AC displayed mitochondrial dysfunction that could contribute to secondary injury events and trigger long-term degenerative changes. Phosphoproteome analysis in these zones revealed that certain differentially phosphorylated proteins synergistically contribute to the injury events along with the differentially expressed proteins. Non-synaptic mitochondria (ns-mito) was associated with relatively more differentially expressed proteins (DEPs) compared to synaptosomes (Syn), while the latter displayed increased protein oxidation including tryptophan (Trp) oxidation. Proteomic analysis of immunocaptured complex I (CI) from Syn revealed increased Trp oxidation in Ct > PC > AC (vs. control). Oxidized W272 in the ND1 subunit of CI, revealed local conformational changes in ND1 and the neighboring subunits, as indicated by molecular dynamics simulation (MDS). Taken together, neuroanatomical zones in TBI show distinct protein profile and protein oxidation representing different primary and secondary injury events with potential implications for TBI pathology and neurological status of the patients.
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Affiliation(s)
- Niya Gowthami
- Department of Clinical Psychopharmacology and Neurotoxicology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Nithya Pursotham
- Department of Clinical Psychopharmacology and Neurotoxicology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Gourav Dey
- Proteomics and Bioinformatics Laboratory, Neurobiology Research Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
- Institute of Bioinformatics, Bengaluru, India
| | - Vivek Ghose
- Proteomics and Bioinformatics Laboratory, Neurobiology Research Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
- Institute of Bioinformatics, Bengaluru, India
| | - Gajanan Sathe
- Proteomics and Bioinformatics Laboratory, Neurobiology Research Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
- Institute of Bioinformatics, Bengaluru, India
| | - Nupur Pruthi
- Department of Neurosurgery, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Dhaval Shukla
- Department of Neurosurgery, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Narayanappa Gayathri
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Rashmi Santhoshkumar
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Balasundaram Padmanabhan
- Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Vivek Chandramohan
- Department of Biotechnology, Siddaganga Institute of Technology (SIT), Tumakuru, India
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - M M Srinivas Bharath
- Department of Clinical Psychopharmacology and Neurotoxicology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
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5
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Joshi N, Bhat F, Bellad A, Sathe G, Jain A, Chavan S, Sirdeshmukh R, Pandey A. Urinary Proteomics for Discovery of Gastric Cancer Biomarkers to Enable Precision Clinical Oncology. OMICS 2023; 27:361-371. [PMID: 37579183 PMCID: PMC10625469 DOI: 10.1089/omi.2023.0077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
For precision in clinical oncology practice, detection of tumor-derived peptides and proteins in urine offers an attractive and noninvasive alternative for diagnostic or screening purposes. In this study, we report comparative quantitative proteomic profiling of urine samples from patients with gastric cancer and healthy controls using tandem mass tags-based multiplexed mass spectrometry approach. We identified 1504 proteins, of which 246 were differentially expressed in gastric cancer cases. Notably, ephrin A1 (EFNA1), pepsinogen A3 (PGA3), sortilin 1 (SORT1), and vitronectin (VTN) were among the upregulated proteins, which are known to play crucial roles in the progression of gastric cancer. We also found other overexpressed proteins, including shisa family member 5 (SHISA5), mucin like 1 (MUCL1), and leukocyte cell derived chemotaxin 2 (LECT2), which had not previously been linked to gastric cancer. Using a novel approach for targeted proteomics, SureQuant, we validated changes in abundance of a subset of proteins discovered in this study. We confirmed the overexpression of vitronectin and sortilin 1 in an independent set of urine samples. Altogether, this study provides molecular candidates for biomarker development in gastric cancer, and the findings also support the promise of urinary proteomics for noninvasive diagnostics and personalized/precision medicine in the oncology clinic.
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Affiliation(s)
- Neha Joshi
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Firdous Bhat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Anikha Bellad
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Anu Jain
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sandip Chavan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ravi Sirdeshmukh
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Akhilesh Pandey
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
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6
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Simpson LM, Fulcher LJ, Sathe G, Brewer A, Zhao JF, Squair DR, Crooks J, Wightman M, Wood NT, Gourlay R, Varghese J, Soares RF, Sapkota GP. An affinity-directed phosphatase, AdPhosphatase, system for targeted protein dephosphorylation. Cell Chem Biol 2023; 30:188-202.e6. [PMID: 36720221 DOI: 10.1016/j.chembiol.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 11/07/2022] [Accepted: 01/10/2023] [Indexed: 02/02/2023]
Abstract
Reversible protein phosphorylation, catalyzed by protein kinases and phosphatases, is a fundamental process that controls protein function and intracellular signaling. Failure of phospho-control accounts for many human diseases. While a kinase phosphorylates multiple substrates, a substrate is often phosphorylated by multiple kinases. This renders phospho-control at the substrate level challenging, as it requires inhibition of multiple kinases, which would thus affect other kinase substrates. Here, we describe the development and application of the affinity-directed phosphatase (AdPhosphatase) system for targeted dephosphorylation of specific phospho-substrates. By deploying the Protein Phosphatase 1 or 2A catalytic subunits conjugated to an antigen-stabilized anti-GFP nanobody, we can promote the dephosphorylation of two independent phospho-proteins, FAM83D or ULK1, knocked in with GFP-tags using CRISPR-Cas9, with exquisite specificity. By redirecting protein phosphatases to neo-substrates through nanobody-mediated proximity, AdPhosphatase can alter the phospho-status and function of target proteins and thus, offers a new modality for potential drug discovery approaches.
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Affiliation(s)
- Luke M Simpson
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Luke J Fulcher
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Gajanan Sathe
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Abigail Brewer
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jin-Feng Zhao
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Daniel R Squair
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jennifer Crooks
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Melanie Wightman
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Nicola T Wood
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Robert Gourlay
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Joby Varghese
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Renata F Soares
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Gopal P Sapkota
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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7
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George IA, Sathe G, Ghose V, Chougule A, Chandrani P, Patil V, Noronha V, Venkataramanan R, Limaye S, Pandey A, Prabhash K, Kumar P. Integrated proteomics and phosphoproteomics revealed druggable kinases in neoadjuvant chemotherapy resistant tongue cancer. Front Cell Dev Biol 2022; 10:957983. [PMID: 36393868 PMCID: PMC9651967 DOI: 10.3389/fcell.2022.957983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/04/2022] [Indexed: 03/27/2024] Open
Abstract
Tongue squamous cell carcinoma is an aggressive oral cancer with a high incidence of metastasis and poor prognosis. Most of the oral cavity cancer patients present in clinics with locally advanced unresectable tumors. Neoadjuvant treatment is beneficial for these individuals as it reduces the tumor size aiding complete resection. However, patients develop therapy resistance to the drug regimen. In this study, we explored the differential expression of proteins and altered phosphorylation in the neoadjuvant chemotherapy resistant tongue cancer patients. We integrated the proteomic and phosphoproteomic profiles of resistant (n = 4) and sensitive cohorts (n = 4) and demonstrated the differential expression and phosphorylation of proteins in the primary tissue of the respective subject groups. We observed differential and extensive phosphorylation of keratins such as KRT10 and KRT1 between the two cohorts. Furthermore, our study revealed a kinase signature associated with neoadjuvant chemotherapy resistance. Kinases such as MAPK1, AKT1, and MAPK3 are predicted to regulate the resistance in non-responders. Pathway analysis showed enrichment of Rho GTPase signaling and hyperphosphosphorylation of proteins involved in cell motility, invasion, and drug resistance. Targeting the kinases could help with the clinical management of neoadjuvant chemotherapy-resistant tongue cancer.
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Affiliation(s)
- Irene A. George
- Institute of Bioinformatics, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Gajanan Sathe
- Institute of Bioinformatics, Bangalore, India
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Vivek Ghose
- Institute of Bioinformatics, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | | | | | | | | | | | - Sewanti Limaye
- Sir H.N. Reliance Foundation Hospital and Research Centre, Mumbai, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
- Department of Laboratory Medicine and Pathology, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | | | - Prashant Kumar
- Institute of Bioinformatics, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Karkinos Healthcare Pvt Ltd., Mumbai, India
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8
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Amit C, Ghose V, Narayanan J, Padmanabhan P, Sathe G, Elchuri S. Phosphoprotein network analysis of corneal epithelium of Keratoconus patients. Proteomics 2022; 22:e2100416. [PMID: 35776780 DOI: 10.1002/pmic.202100416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 06/16/2022] [Accepted: 06/28/2022] [Indexed: 11/10/2022]
Abstract
Keratoconus (KC) is non-inflammatory, bilateral progressive corneal ectasia, and a disease of established biomechanical instability. The etiology of KC is believed to be multifactorial. Although previous studies gained insight into the understanding of the disease, little is known thus far on global protein phosphorylation changes in Keratoconus. We performed phosphoproteome analysis of corneal epithelium from control (n = 5) and KC patients. Tandem mass tag (TMT) multiplexing technology along with immobilized metal affinity chromatography (IMAC) were used for the phosphopeptides enrichment and quantitation. Enriched peptides were analyzed on Orbitrap Fusion Tribrid mass spectrometer. This leads to the identification of 2939 unique phosphopeptides derived from 1270 proteins. We observed significant differential phosphorylation of 591 phosphopeptides corresponding to 375 proteins. Our results provide first phosphoproteomic signature of the Keratoconus disease and identified dysregulated signalling pathways that can be targeted for therapy in future studies. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Chatterjee Amit
- Department of Nanobiotechnology, Vision Research Foundation, Sankara Nethralaya Campus, Chennai, India
| | - Vivek Ghose
- Institute of Bioinformatics, Bangalore, Karnataka, India
| | - Jankiraman Narayanan
- Department of Nanobiotechnology, Vision Research Foundation, Sankara Nethralaya Campus, Chennai, India
| | - Prema Padmanabhan
- Department of Cornea, Medical Research Foundation Sankara Nethralaya, Chennai, India
| | - Gajanan Sathe
- Institute of Bioinformatics, Bangalore, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Sailaja Elchuri
- Department of Nanobiotechnology, Vision Research Foundation, Sankara Nethralaya Campus, Chennai, India
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9
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Ganesh RA, Sonpatki P, Naik D, John AE, Sathe G, Lakshmikantha A, Chandrachari KP, Bauer L, Knäuper V, Aeschlimann D, Venkatraaman K, Shah N, Sirdeshmukh R. Multi-Omics Analysis of Glioblastoma and Glioblastoma Cell Line: Molecular Insights Into the Functional Role of GPR56 and TG2 in Mesenchymal Transition. Front Oncol 2022; 12:841890. [PMID: 35600402 PMCID: PMC9119646 DOI: 10.3389/fonc.2022.841890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
G protein-coupled receptor 56 (GPR56/ADGRG1) is an adhesion GPCR with an essential role in brain development and cancer. Elevated expression of GPR56 was observed in the clinical specimens of Glioblastoma (GBM), a highly invasive primary brain tumor. However, we found the expression to be variable across the specimens, presumably due to the intratumor heterogeneity of GBM. Therefore, we re-examined GPR56 expression in public domain spatial gene expression data and single-cell expression data for GBM, which revealed that GPR56 expression was high in cellular tumors, infiltrating tumor cells, and proliferating cells, low in microvascular proliferation and peri-necrotic areas of the tumor, especially in hypoxic mesenchymal-like cells. To gain a better understanding of the consequences of GPR56 downregulation in tumor cells and other molecular changes associated with it, we generated a sh-RNA-mediated GPR56 knockdown in the GBM cell line U373 and performed transcriptomics, proteomics, and phospho-proteomics analysis. Our analysis revealed enrichment of gene signatures, pathways, and phosphorylation of proteins potentially associated with mesenchymal (MES) transition in the tumor and concurrent increase in cell invasion and migration behavior of the GPR56 knockdown GBM cells. Interestingly, our analysis also showed elevated expression of Transglutaminase 2 (TG2) - a known interactor of GPR56, in the knockdown cells. The inverse expression of GPR56 and TG2 was also observed in intratumoral, spatial gene expression data for GBM and in GBM cell lines cultured in vitro under hypoxic conditions. Integrating all these observations, we propose a putative functional link between the inverse expression of the two proteins, the hypoxic niche and the mesenchymal status in the tumor. Hypoxia-induced downregulation of GPR56 and activation of TG2 may result in a network of molecular events that contribute to the mesenchymal transition of GBM cells, and we propose a putative model to explain this functional and regulatory relationship of the two proteins.
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Affiliation(s)
- Raksha A Ganesh
- Mazumdar Shaw Center for Translational Research, Narayana Health, Bangalore, India.,Center for Bio-Separation Technology, Vellore Institute of Technology, Vellore, India
| | - Pranali Sonpatki
- Mazumdar Shaw Center for Translational Research, Narayana Health, Bangalore, India
| | - Divya Naik
- Mazumdar Shaw Center for Translational Research, Narayana Health, Bangalore, India
| | | | - Gajanan Sathe
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | | | | | - Lea Bauer
- Matrix Biology and Tissue Repair Research Unit, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, United Kingdom
| | - Vera Knäuper
- Matrix Biology and Tissue Repair Research Unit, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, United Kingdom
| | - Daniel Aeschlimann
- Matrix Biology and Tissue Repair Research Unit, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, United Kingdom
| | - Krishnan Venkatraaman
- Center for Bio-Separation Technology, Vellore Institute of Technology, Vellore, India
| | - Nameeta Shah
- Mazumdar Shaw Center for Translational Research, Narayana Health, Bangalore, India
| | - Ravi Sirdeshmukh
- Mazumdar Shaw Center for Translational Research, Narayana Health, Bangalore, India.,Institute of Bioinformatics, International Tech Park, Bangalore, India.,Health Sciences, Manipal Academy of Higher Education, Manipal, India
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10
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Jain AP, Sambath J, Sathe G, George IA, Pandey A, Thompson EW, Kumar P. Pan-cancer quantitation of epithelial-mesenchymal transition dynamics using parallel reaction monitoring-based targeted proteomics approach. J Transl Med 2022; 20:84. [PMID: 35148768 PMCID: PMC8832824 DOI: 10.1186/s12967-021-03227-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/30/2021] [Indexed: 12/31/2022] Open
Abstract
Epithelial–mesenchymal transition (EMT) is a dynamic and complex cellular process that is known to be hijacked by cancer cells to facilitate invasion, metastasis and therapeutic resistance. Several quantitative measures to assess the interplay between EMT and cancer progression are available, based on large scale genome and transcriptome data. However, these large scale multi-omics studies have repeatedly illustrated a lack of correlation in mRNA and protein abundances that may be influenced by diverse post-translational regulation. Hence, it is imperative to understand how changes in the EMT proteome are associated with the process of oncogenic transformation. To this effect, we developed a parallel reaction monitoring-based targeted proteomics method for quantifying abundances of EMT-associated proteins across cancer cell lines. Our study revealed that quantitative measurement of EMT proteome which enabled a more accurate assessment than transcriptomics data and revealed specific discrepancies against a backdrop of generally strong concordance between proteomic and transcriptomic data. We further demonstrated that changes in our EMT proteome panel might play a role in tumor transformation across cancer types. In future, this EMT panel assay has the potential to be used for clinical samples to guide treatment choices and to congregate functional information for the development and advancing novel therapeutics.
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Affiliation(s)
- Ankit P Jain
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India
| | - Janani Sambath
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India
| | - Irene A George
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India.,Department of Laboratory Medicine and Pathology, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Erik W Thompson
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, 4059, Australia. .,School-Biomedical Sciences, Translational Research Institute, Woolloongabba, QLD, 4102, Australia.
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India. .,Manipal Academy of Higher Education (MAHE), Manipal, 576104, India. .,Somaiya Institute of Research and Consultancy (SIRAC), Somaiya Vidyavihar University (SVU), Vidyavihar, Mumbai, 400077, Maharashtra, India.
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11
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Amit C, Sathe G, Shunmugam A, Athyala PK, Ghose V, Chitipothu S, Janakiraman N, Sundara R, Elchuri SV. Graphitic Carbon Nitride Causes Widespread Global Molecular Changes in Epithelial and Fibroblast Cells. ACS Omega 2021; 6:9368-9380. [PMID: 33869917 PMCID: PMC8047657 DOI: 10.1021/acsomega.0c05513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
For scaffold and imaging applications, nanomaterials such as graphene and its derivatives have been widely used. Graphitic carbon nitride (g-C3N4) is among one such derivative of graphenes, which draws strong consideration due to its physicochemical properties and photocatalytic activity. To use g-C3N4 for biological applications, such as molecular imaging or drug delivery, it must interact with the epithelium, cross the epithelial barrier, and then come in contact with the extracellular matrix of the fibroblast cells. Thus, it becomes essential to understand its molecular mechanism of action. Hence, in this study, to understand the molecular reprogramming associated with g-C3N4, global gene expression using DNA microarrays and proteomics using tandem mass tag (TMT) labeling and mass spectrometry were performed in epithelial and fibroblast cells, respectively. Our results showed that g-C3N4 can cross the epithelial barrier by regulating the adherens junction proteins. Further, using g-C3N4-PDMS scaffolds as a mimic of the extracellular matrix for fibroblast cells, the common signaling pathways were identified between the epithelium and fibroblast cells. These pathways include Wnt signaling, integrin signaling, TGF-β signaling, cadherin signaling, oxidative stress response, ubiquitin proteasome pathway, and EGF receptor signaling pathways. These altered signature pathways identified could play a prominent role in g-C3N4-mediated cellular interactions in both epithelial and fibroblast cells. Additionally, β catenin, EGFR, and MAP2K2 protein-protein interaction networks could play a prominent role in fibroblast cell proliferation. The findings could further our knowledge on g-C3N4-mediated alterations in cellular molecular signatures, enabling the potential use of these materials for biological applications such as molecular imaging and drug delivery.
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Affiliation(s)
- Chatterjee Amit
- Department
of Nanobiotechnology, Vision Research Foundation, Chennai 600006, India
| | - Gajanan Sathe
- Institute
of Bioinformatics, Bangalore 560066, Karnataka, India
- Manipal
Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Abinaya Shunmugam
- Department
of Physics, Indian Institute of Technology,
Madras, Chennai 600036, India
| | | | - Vivek Ghose
- Institute
of Bioinformatics, Bangalore 560066, Karnataka, India
| | - Srujana Chitipothu
- Central
Research Instrumentation Facility, Core Lab, Vision Research Foundation, Chennai 600006, India
| | | | - Ramaprabhu Sundara
- Department
of Physics, Indian Institute of Technology,
Madras, Chennai 600036, India
| | - Sailaja V. Elchuri
- Department
of Nanobiotechnology, Vision Research Foundation, Chennai 600006, India
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12
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Abstract
Alzheimer’s disease (AD) is the most prevalent form of dementia, and the numbers of AD patients are expected to increase as human life expectancy improves. Deposition of β-amyloid protein (Aβ) in the extracellular matrix and intracellular neurofibrillary tangles are molecular hallmarks of the disease. Since the precise pathophysiology of AD has not been elucidated yet, effective treatment is not available. Thus, understanding the disease pathology, as well as identification and development of valid biomarkers, is imperative for early diagnosis as well as for monitoring disease progression and therapeutic responses. Keeping this goal in mind several studies using quantitative proteomics platform have been carried out on both clinical specimens including the brain, cerebrospinal fluid (CSF), plasma and on animal models of AD. In this review, we summarize the mass spectrometry (MS)-based proteomics studies on AD and discuss the discovery as well as validation stages in brief to identify candidate biomarkers.
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Affiliation(s)
- Ankit P. Jain
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
- Correspondence:
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13
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Sathe G, Albert M, Darrow J, Saito A, Troncoso J, Pandey A, Moghekar A. Quantitative proteomic analysis of the frontal cortex in Alzheimer's disease. J Neurochem 2021; 156:988-1002. [PMID: 32614981 PMCID: PMC7775912 DOI: 10.1111/jnc.15116] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022]
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease characterized by intracellular formation of neurofibrillary tangles and extracellular deposition of β-amyloid protein (Aβ) in the extracellular matrix. The pathogenesis of AD has not yet been fully elucidated and little is known about global alterations in the brain proteome that are related to AD. To identify and quantify such AD-related changes in the brain, we employed a tandem mass tags approach coupled to high-resolution mass spectrometry. We compared the proteomes of frontal cortex from AD patients with corresponding age-matched brain samples. Liquid chromatography-mass spectrometry/MS analysis carried out on an Orbitrap Fusion Lumos Tribrid mass spectrometer led to identification of 8,066 proteins. Of these, 432 proteins were observed to be significantly altered (>1.5 fold) in their expression in AD brains. Proteins whose abundance was previously known to be altered in AD were identified including secreted phosphoprotein 1 (SPP1), somatostatin (SST), SPARC-related modular calcium binding 1 (SMOC1), dual specificity phosphatase 26 (DUSP26), and neuronal pentraxin 2 (NPTX2). In addition, we identified several novel candidates whose association with AD has not been previously described. Of the novel molecules, we validated chromogranin A (CHGA), inner membrane mitochondrial protein (IMMT) and RAS like proto-oncogene A (RALA) in an additional set of 20 independent brain samples using targeted parallel reaction monitoring mass spectrometry assays. The differentially expressed proteins discovered in our study, once validated in larger cohorts, should help discern the pathogenesis of AD.
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Affiliation(s)
- Gajanan Sathe
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Marilyn Albert
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Jacqueline Darrow
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Atsushi Saito
- Department of Pathology and Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Juan Troncoso
- Department of Pathology and Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
- Current address: Department of Laboratory Medicine and Pathology, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Abhay Moghekar
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
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14
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Gondkar K, Sathe G, Joshi N, Nair B, Pandey A, Kumar P. Integrated Proteomic and Phosphoproteomics Analysis of DKK3 Signaling Reveals Activated Kinase in the Most Aggressive Gallbladder Cancer. Cells 2021; 10:cells10030511. [PMID: 33670899 PMCID: PMC7997438 DOI: 10.3390/cells10030511] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/31/2022] Open
Abstract
DKK3 is a secreted protein, which belongs to a family of Wnt antagonists and acts as a potential tumor suppressor in gallbladder cancer. To further understand its tumor suppressor functions, we overexpressed DKK3 in 3 GBC cell lines. We have employed high-resolution mass spectrometry and tandem mass tag (TMT) multiplexing technology along with immobilized metal affinity chromatography to enrich phosphopeptides to check the downstream regulators. In this study, we reported for the first time the alteration in the phosphorylation of 14 kinases upon DKK3 overexpression. In addition, we observed DKK3 induced hyper phosphorylation of 2 phosphatases: PPP1R12A and PTPRA, which have not been reported previously. Canonical pathway analysis of altered molecules indicated differential enrichment of signaling cascades upon DKK3 overexpression in all the 3 cell lines. Protein kinase A signaling, Sirtuin signaling pathway, and Cell Cycle Control of Chromosomal Replication were observed to be differentially activated in the GBC cell lines. Our study revealed, DKK3 overexpression has differential effect based on the aggressive behavior of the cell lines. This study expands the understanding of DKK3-mediated signaling events and can be used as a primary factor for understanding the complex nature of this molecule.
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Affiliation(s)
- Kirti Gondkar
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India; (K.G.); (G.S.); (N.J.)
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India;
| | - Gajanan Sathe
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India; (K.G.); (G.S.); (N.J.)
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India;
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Neha Joshi
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India; (K.G.); (G.S.); (N.J.)
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India;
| | - Akhilesh Pandey
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India;
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Prashant Kumar
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India; (K.G.); (G.S.); (N.J.)
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India;
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
- Correspondence:
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15
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Sathe G, Deepha S, Gayathri N, Nagappa M, Parayil Sankaran B, Taly AB, Khanna T, Pandey A, Govindaraj P. Ethylmalonic encephalopathy ETHE1 p. D165H mutation alters the mitochondrial function in human skeletal muscle proteome. Mitochondrion 2021; 58:64-71. [PMID: 33639274 DOI: 10.1016/j.mito.2021.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/19/2021] [Accepted: 02/12/2021] [Indexed: 01/01/2023]
Abstract
Ethylmalonic encephalopathy (EE) is a rare autosomal recessive inborn error of metabolism. To study the molecular effects of ETHE1 p. D165H mutation, we employed mass spectrometry-based mitochondrial proteome and phosphoproteome profiling in the human skeletal muscle. Eighty-six differentially altered proteins were identified, of which thirty-seven mitochondrial proteins were differentially expressed, and most of the proteins (37%) were down-regulated in the OXPHOS complex-IV. Also, nine phosphopeptides that correspond to eight mitochondrial proteins were significantly affected in EE patient. These altered proteins recognized are involved in several pathways and molecular functions, predominantly in oxidoreductase activity. This is the first study that has integrated proteome and phosphoproteome of skeletal muscle and identified multiple proteins associated in the pathogenesis of EE.
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Affiliation(s)
- Gajanan Sathe
- Institute of Bioinformatics, International Tech Park, Bangalore, India; Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Manipal Academy of Higher Education, Manipal, India
| | - Sekar Deepha
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Neuromuscular Laboratory, Neurobiology Research Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Narayanappa Gayathri
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Neuromuscular Laboratory, Neurobiology Research Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Madhu Nagappa
- Neuromuscular Laboratory, Neurobiology Research Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Bindu Parayil Sankaran
- Neuromuscular Laboratory, Neurobiology Research Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Genetic Metabolic Disorders Services, Children's Hospital at Westmead, NSW, Australia; The Children's Hospital at Westmead Clinical School, Sydney Medical School, The Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Arun B Taly
- Neuromuscular Laboratory, Neurobiology Research Center, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Tripti Khanna
- Indian Council of Medical Research (ICMR), New Delhi, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Tech Park, Bangalore, India; Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Manipal Academy of Higher Education, Manipal, India
| | - Periyasamy Govindaraj
- Institute of Bioinformatics, International Tech Park, Bangalore, India; Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Manipal Academy of Higher Education, Manipal, India.
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16
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Thakur G, Sathe G, Kundu I, Biswas B, Gautam P, Alkahtani S, Idicula-Thomas S, Sirdeshmukh R, Kishore U, Madan T. Membrane Interactome of a Recombinant Fragment of Human Surfactant Protein D Reveals GRP78 as a Novel Binding Partner in PC3, a Metastatic Prostate Cancer Cell Line. Front Immunol 2021; 11:600660. [PMID: 33542717 PMCID: PMC7850985 DOI: 10.3389/fimmu.2020.600660] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 12/15/2020] [Indexed: 01/08/2023] Open
Abstract
Surfactant protein-D (SP-D), a member of the collectin family has been shown to induce apoptosis in cancer cells. SP-D is composed of an N-terminal collagen-like domain and a calcium-dependent carbohydrate recognition domain (CRD). Recently, we reported that a recombinant fragment of human SP-D (rfhSP-D), composed of homotrimeric CRD region, induced intrinsic apoptotic pathway in prostate cancer cells. Here, we analyzed the membrane interactome of rfhSP-D in an androgen-independent prostate cancer cell line, PC3, by high resolution mass spectrometry and identified 347 proteins. Computational analysis of PPI network of this interactome in the context of prostate cancer metastasis and apoptosis revealed Glucose Regulated Protein of 78 kDa (GRP78) as an important binding partner of rfhSP-D. Docking studies suggested that rfhSP-D (CRD) bound to the substrate-binding domain of glycosylated GRP78. This was further supported by the observations that human recombinant GRP78 interfered with the binding of rfhSP-D to anti-SP-D polyclonal antibodies; GRP78 also significantly inhibited the binding of recombinant full-length human SP-D with a monoclonal antibody specific to the CRD in a dose-dependent manner. We conclude that the interaction with rfhSP-D is likely to interfere with the pro-survival signaling of GRP78.
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Affiliation(s)
- Gargi Thakur
- Department of Innate Immunity, Indian Council of Medical Research (ICMR)-National Institute for Research in Reproductive Health, Mumbai, India
| | - Gajanan Sathe
- Institute of Bioinformatics, Bengaluru, India.,Manipal Academy of Higher Education, Manipal, India
| | - Indra Kundu
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai, India
| | - Barnali Biswas
- Department of Innate Immunity, Indian Council of Medical Research (ICMR)-National Institute for Research in Reproductive Health, Mumbai, India
| | - Poonam Gautam
- Laboratory of Molecular Oncology, ICMR-National Institute of Pathology, New Delhi, India
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Susan Idicula-Thomas
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai, India
| | - Ravi Sirdeshmukh
- Institute of Bioinformatics, Bengaluru, India.,Manipal Academy of Higher Education, Manipal, India
| | - Uday Kishore
- Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Taruna Madan
- Department of Innate Immunity, Indian Council of Medical Research (ICMR)-National Institute for Research in Reproductive Health, Mumbai, India
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17
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Babu N, Pinto SM, Biswas M, Subbannayya T, Rajappa M, Mohan SV, Advani J, Rajagopalan P, Sathe G, Syed N, Radhakrishna VD, Muthusamy O, Navani S, Kumar RV, Gopisetty G, Rajkumar T, Radhakrishnan P, Thiyagarajan S, Pandey A, Gowda H, Majumder P, Chatterjee A. Phosphoproteomic analysis identifies CLK1 as a novel therapeutic target in gastric cancer. Gastric Cancer 2020; 23:796-810. [PMID: 32333232 DOI: 10.1007/s10120-020-01062-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Phosphorylation is an important regulatory mechanism of protein activity in cells. Studies in various cancers have reported perturbations in kinases resulting in aberrant phosphorylation of oncoproteins and tumor suppressor proteins. METHODS In this study, we carried out quantitative phosphoproteomic analysis of gastric cancer tissues and corresponding xenograft samples. Using these data, we employed bioinformatics analysis to identify aberrant signaling pathways. We further performed molecular inhibition and silencing of the upstream regulatory kinase in gastric cancer cell lines and validated its effect on cellular phenotype. Through an ex vivo technology utilizing patient tumor and blood sample, we sought to understand the therapeutic potential of the kinase by recreating the tumor microenvironment. RESULTS Using mass spectrometry-based high-throughput analysis, we identified 1,344 phosphosites and 848 phosphoproteins, including differential phosphorylation of 177 proteins (fold change cut-off ≥ 1.5). Our data showed that a subset of differentially phosphorylated proteins belonged to splicing machinery. Pathway analysis highlighted Cdc2-like kinase (CLK1) as upstream kinase. Inhibition of CLK1 using TG003 and CLK1 siRNA resulted in a decreased cell viability, proliferation, invasion and migration as well as modulation in the phosphorylation of SRSF2. Ex vivo experiments which utilizes patient's own tumor and blood to recreate the tumor microenvironment validated the use of CLK1 as a potential target for gastric cancer treatment. CONCLUSIONS Our data indicates that CLK1 plays a crucial role in the regulation of splicing process in gastric cancer and that CLK1 can act as a novel therapeutic target in gastric cancer.
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Affiliation(s)
- Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India
| | - Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed To Be University), Mangalore, 575018, India
| | | | - Tejaswini Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Mitra Biotech, Bangalore, 560100, India
| | | | - Sonali V Mohan
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Pavithra Rajagopalan
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | | | | | | | - Rekha V Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, 560029, India
| | - Gopal Gopisetty
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India
| | - Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India
| | | | | | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India.,Cancer Precision Medicine, QIMR Berghofer, Royal Brisbane Hospital, Brisbane, QLD, 4029, Australia
| | | | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India. .,Manipal Academy of Higher Education, Manipal, 576104, India. .,Mitra Biotech, Bangalore, 560100, India.
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18
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Sathe G, George IA, Deb B, Jain AP, Patel K, Nayak B, Karmakar S, Seth A, Pandey A, Kumar P. Urinary glycoproteomic profiling of non-muscle invasive and muscle invasive bladder carcinoma patients reveals distinct N-glycosylation pattern of CD44, MGAM, and GINM1. Oncotarget 2020; 11:3244-3255. [PMID: 32922663 PMCID: PMC7456616 DOI: 10.18632/oncotarget.27696] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Clinical management of bladder carcinomas (BC) remains a major challenge and demands comprehensive multi-omics analysis for better stratification of the disease. Identification of patients on risk requires identification of signatures predicting prognosis risk of the patients. Understanding the molecular alterations associated with the disease onset and progression could improve the routinely used diagnostic and therapy procedures. In this study, we investigated the aberrant changes in N-glycosylation pattern of proteins associated with tumorigenesis as well as disease progression in bladder cancer. We integrated and compared global N-glycoproteomic and proteomic profile of urine samples from bladder cancer patients at different clinicopathological stages (non-muscle invasive and muscle-invasive patients [n = 5 and 4 in each cohort]) with healthy subjects (n = 5) using SPEG method. We identified 635 N-glycopeptides corresponding to 381 proteins and 543 N-glycopeptides corresponding to 326 proteins in NMIBC and MIBC patients respectively. Moreover, we identified altered glycosylation in 41 NMIBC and 21 MIBC proteins without any significant change in protein abundance levels. In concordance with the previously published bladder cancer cell line N-glycoproteomic data, we also observed dysregulated glycosylation in ECM related proteins. Further, we identified distinct N-glycosylation pattern of CD44, MGAM, and GINM1 between NMIBC and MIBC patients, which may be associated with disease progression in bladder cancer. These aberrant protein glycosylation events would provide a novel approach for bladder carcinoma diagnosis and further define novel mechanisms of tumor initiation and progression.
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Affiliation(s)
- Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore 560029, India.,These authors contributed equally to this work and share the first authorship
| | - Irene A George
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, India.,These authors contributed equally to this work and share the first authorship
| | - Barnali Deb
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, India.,These authors contributed equally to this work and share the second authorship
| | - Ankit P Jain
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,These authors contributed equally to this work and share the second authorship
| | - Krishna Patel
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Brusabhanu Nayak
- Department of Urology, All India Institute of Medical Sciences, New Delhi 110070, India
| | - Subhradip Karmakar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110070, India
| | - Amlesh Seth
- Department of Urology, All India Institute of Medical Sciences, New Delhi 110070, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore 560029, India.,Department of Laboratory Medicine and Pathology, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, India
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19
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Gangadharappa BS, Rajashekarappa S, Sathe G. Proteomic profiling of Serratia marcescens by high-resolution mass spectrometry. ACTA ACUST UNITED AC 2020; 10:123-135. [PMID: 32363156 PMCID: PMC7186543 DOI: 10.34172/bi.2020.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/07/2019] [Accepted: 09/03/2019] [Indexed: 11/09/2022]
Abstract
Introduction: Serratia marcescens, an opportunistic human pathogen, is reported as an important cause of nosocomial infection and outbreaks. Although the genome of S. marcescens (ATCC 13880) was completely sequenced by 2014, there are no studies on the proteomic profile of the organism. The objective of the present study is to analyze the protein profile of S. marcescens (ATCC 13880) using a high resolution mass spectrometry (MS). Methods: Serratia marcescens ATCC 13880 strain was grown in Luria-Bertani broth and the protein extracted was subjected to trypsin digestion, followed by basic reverse phase liquid chromatography fractionation. The peptide fractions were then analysed using Orbitrap Fusion Mass Spectrometry and the raw MS data were processed in Proteome Discoverer software. Results: The proteomic analysis identified 15 009 unique peptides mapping to 2541 unique protein groups, which corresponds to approximately 54% of the computationally predicted protein-coding genes. Bioinformatic analysis of these identified proteins showed their involvement in biological processes such as cell wall organization, chaperone-mediated protein folding and ATP binding. Pathway analysis revealed that some of these proteins are associated with bacterial chemotaxis and beta-lactam resistance pathway. Conclusion: To the best of our knowledge, this is the first high-throughput proteomics study of S. marcescens (ATCC 13880). These novel observations provide a crucial baseline molecular profile of the S. marcescens proteome which will prove to be helpful for the future research in understanding the host-pathogen interactions during infection, elucidating the mechanism of multidrug resistance, and developing novel diagnostic markers or vaccine for the disease.
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Affiliation(s)
- Bhavya Somalapura Gangadharappa
- Department of Biotechnology, M.S. Ramaiah Institute of Technology, Bengaluru-560054, Karnataka, India.,Visvesvaraya Technological University, Belagavi-590018, Karnataka, India
| | | | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore-560066, Karnataka, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore-560029, Karnataka, India
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20
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Na CH, Sathe G, Rosenthal LS, Moghekar AR, Dawson VL, Dawson TM, Pandey A. Development of a novel method for the quantification of tyrosine 39 phosphorylated α- and β-synuclein in human cerebrospinal fluid. Clin Proteomics 2020; 17:13. [PMID: 32390785 PMCID: PMC7197159 DOI: 10.1186/s12014-020-09277-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 04/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder. Biomarkers that can help monitor the progression of PD or response to disease-modifying agents will be invaluable in making appropriate therapeutic decisions. Further, biomarkers that could be used to distinguish PD from other related disorders with PD-like symptoms will be useful for accurate diagnosis and treatment. C-Abl tyrosine kinase is activated in PD resulting in increased phosphorylation of the tyrosine residue at position 39 (Y39) of α-synuclein (α-syn) (pY39 α-syn), which contributes to the death of dopaminergic neurons. Because pY39 α-syn may be pathogenic, monitoring pY39 α-syn could allow us to diagnose presymptomatic PD and help monitor disease progression and response to treatment. We sought to investigate if increased phosphorylation of pY39 α-syn can be detected in the cerebrospinal fluid (CSF) of PD patients by targeted mass spectrometry. METHODS Here, we report a two-step enrichment method in which phosphotyrosine peptides were first enriched with an anti-phosphotyrosine antibody followed by a second round of enrichment by titanium dioxide (TiO2) beads to detect EGVLpYVGSK sequence derived from tyrosine 39 region of α- and β-synuclein (αβ-syn). Accurate quantification was achieved by adding a synthetic heavy version of pY39 αβ-syn peptide before enzymatic digestion. RESULTS Using the developed enrichment methods and optimized parallel reaction monitoring (PRM) assays, we detected pY39 αβ-syn peptide in human CSF and demonstrated that the ratio of pY39 αβ-syn to Y39 αβ-syn was significantly increased in the CSF of patients with PD. CONCLUSIONS We anticipate that this optimized two-step enrichment-based PRM detection method will help monitor c-Abl activation in PD patients and can also be used to quantify other phosphotyrosine peptides of low abundance in biological samples.
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Affiliation(s)
- Chan Hyun Na
- Neurodegeneration Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
| | - Gajanan Sathe
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
- Present Address: Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560 029 India
| | - Liana S. Rosenthal
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Abhay R. Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Valina L. Dawson
- Neurodegeneration Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Ted M. Dawson
- Neurodegeneration Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Akhilesh Pandey
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
- Department of Biological Chemistry, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Manipal Academy of Higher Education (MAHE), Manipal, 576104 Karnataka India
- Present Address: Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
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21
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Patil S, Subbannayya T, Mohan SV, Babu N, Advani J, Sathe G, Rajagopalan P, Patel K, Bhandi S, Solanki H, Sidransky D, Gowda H, Chatterjee A, Ferrari M. Proteomic Changes in Oral Keratinocytes Chronically Exposed to Shisha (Water Pipe). OMICS 2020; 23:86-97. [PMID: 30767727 DOI: 10.1089/omi.2018.0173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Shisha (water pipe) smoking is falsely believed to be a hazard-free habit and has become a major public health concern. Studies have reported shisha smoking to be associated with oral lesions, as well as carcinomas of the lung, esophagus, bladder, and pancreas. A deeper understanding of the underlying molecular mechanisms would contribute to identification of biomarkers for targeted public health screening, therapeutic innovation, and better prognosis of associated diseases. In this study, we have established an in vitro chronic cellular model of shisha-exposed oral keratinocytes to study the effect of shisha on oral cells. Normal nontransformed, immortalized oral keratinocytes were chronically exposed to shisha extract for 8 months. This resulted in significant increase in cellular proliferation and cell invasion in shisha-exposed cells compared to the parental cells. Quantitative proteomic analysis of OKF6/TERT1-Parental and OKF6/TERT1-Shisha cells resulted in the identification of 5515 proteins. Forty-three differentially expressed proteins were found to be common across all conditions. Bioinformatic analysis of the dysregulated proteins identified in the proteomic study revealed dysregulation of interferon pathway, upregulation of proteins involved in cell growth, and downregulation of immune processes. The present findings reveal that chronic exposure of normal oral keratinocytes to shisha leads to cellular transformation and dysregulation of immune response. To the best of our knowledge, this is the first report that has developed a model of oral keratinocytes chronically exposed to shisha and identified proteomic alterations associated with shisha exposure. However, further research is required to evaluate the health burden of shisha smoking.
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Affiliation(s)
- Shankargouda Patil
- 1 Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy.,2 Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | | | | | - Niraj Babu
- 3 Institute of Bioinformatics, Bangalore, India.,4 Manipal Academy of Higher Education, Manipal, India
| | | | | | | | | | - Shilpa Bhandi
- 5 Department of Restorative Dental Sciences, Division of Operative Dentistry, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | | | - David Sidransky
- 6 Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Harsha Gowda
- 3 Institute of Bioinformatics, Bangalore, India.,4 Manipal Academy of Higher Education, Manipal, India
| | - Aditi Chatterjee
- 3 Institute of Bioinformatics, Bangalore, India.,4 Manipal Academy of Higher Education, Manipal, India
| | - Marco Ferrari
- 1 Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy.,7 Department of Restorative Dentistry, School of Dentistry, University of Leeds, Leeds, West Yorkshire, United Kingdom
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22
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Sathe G, Mangalaparthi KK, Jain A, Darrow J, Troncoso J, Albert M, Moghekar A, Pandey A. Multiplexed Phosphoproteomic Study of Brain in Patients with Alzheimer's Disease and Age-Matched Cognitively Healthy Controls. OMICS 2020; 24:216-227. [PMID: 32182160 DOI: 10.1089/omi.2019.0191] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder caused by neuronal loss that results in cognitive and functional impairment. Formation of neurofibrillary tangles composed of abnormal hyperphosphorylation of tau protein is one of the major pathological hallmarks of AD. Importantly, several neurodegenerative disorders, including AD, are associated with abnormal protein phosphorylation events. However, little is known thus far on global protein phosphorylation changes in AD. We report a phosphoproteomics study examining the frontal gyrus of people with AD and age-matched cognitively normal subjects, using tandem mass tag (TMT) multiplexing technology along with immobilized metal affinity chromatography to enrich phosphopeptides. We identified 4631 phosphopeptides corresponding to 1821 proteins with liquid chromatography-mass spectrometry (MS)/MS analysis on an Orbitrap Fusion Lumos Tribrid mass spectrometer. Of these, 504 phosphopeptides corresponding to 350 proteins were significantly altered in the AD brain: 389 phosphopeptides increased whereas 115 phosphopeptides decreased phosphorylation. We observed significant changes in phosphorylation of known as well as novel molecules. Using targeted parallel reaction monitoring experiments, we validated the phosphorylation of microtubule-associated protein tau and myristoylated alanine-rich protein kinase C substrate (MARCKS) in control and AD (Control = 6, AD = 11) brain samples. In conclusion, our study provides new evidence on alteration of RNA processing and splicing, neurogenesis and neuronal development, and metabotropic glutamate receptor 5 (GRM5) calcium signaling pathways in the AD brain, and it thus offers new insights to accelerate diagnostics and therapeutics innovation in AD.
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Affiliation(s)
- Gajanan Sathe
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India.,Institute of Bioinformatics, Bangalore, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | | | - Ankit Jain
- Institute of Bioinformatics, Bangalore, India
| | - Jacqueline Darrow
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Juan Troncoso
- Department of Pathology and Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marilyn Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Akhilesh Pandey
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India.,Institute of Bioinformatics, Bangalore, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Manipal Academy of Higher Education (MAHE), Manipal, India.,Department of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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23
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Sivadasan P, Gupta MK, Sathe G, Sudheendra H, Sunny SP, Renu D, Hari P, Gowda H, Suresh A, Kuriakose MA, Sirdeshmukh R. Salivary proteins from dysplastic leukoplakia and oral squamous cell carcinoma and their potential for early detection. J Proteomics 2020; 212:103574. [DOI: 10.1016/j.jprot.2019.103574] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/18/2019] [Accepted: 10/29/2019] [Indexed: 12/15/2022]
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24
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Deb B, Patel K, Sathe G, Kumar P. N-Glycoproteomic Profiling Reveals Alteration In Extracellular Matrix Organization In Non-Type Bladder Carcinoma. J Clin Med 2019; 8:jcm8091303. [PMID: 31450586 PMCID: PMC6780497 DOI: 10.3390/jcm8091303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/01/2019] [Accepted: 08/11/2019] [Indexed: 01/03/2023] Open
Abstract
Treatment of advanced and metastatic bladder carcinoma is often ineffective and displays variable clinical outcomes. Studying this aggressive molecular subtype of bladder carcinoma will lead to better understanding of the pathogenesis which may lead to the identification of new therapeutic strategies. The non-type bladder subtype is phenotypically mesenchymal and has mesenchymal features with a high metastatic ability. Post-translational addition of oligosaccharide residues is an important modification that influences cellular functions and contributes to disease pathology. Here, we report the comparative analysis of N-linked glycosylation across bladder cancer subtypes. To analyze the glycosite-containing peptides, we carried out LC-MS/MS-based quantitative proteomic and glycoproteomic profiling. We identified 1299 unique N-linked glycopeptides corresponding to 460 proteins. Additionally, we identified 118 unique N-linked glycopeptides corresponding to 84 proteins to be differentially glycosylated only in non-type subtypes as compared to luminal/basal subtypes. Most of the altered glycoproteins were also observed with changes in their global protein expression levels. However, alterations in 55 differentially expressed glycoproteins showed no significant change at the protein abundance level, representing that the glycosylation site occupancy was changed between the non-type subtype and luminal/basal subtypes. Importantly, the extracellular matrix organization pathway was dysregulated in the non-type subtype of bladder carcinoma. N-glycosylation modifications in the extracellular matrix organization proteins may be a contributing factor for the mesenchymal aggressive phenotype in non-type subtype. These aberrant protein glycosylation would provide additional avenues to employ glycan-based therapies and may lead to the identification of novel therapeutic targets.
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Affiliation(s)
- Barnali Deb
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Krishna Patel
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India.
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India.
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25
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Patil S, Babu N, Subbannayya T, Mohan S, Sathe G, Solanki H, Rajagopalan P, Patel K, Advani J, Bhandi S, Sidransky D, Chatterjee A, Gowda H, Ferrari M. Secretome analysis of oral keratinocytes chronically exposed to shisha. Cancer Biomark 2019; 25:29-41. [DOI: 10.3233/cbm-182099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shankargouda Patil
- Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy
- Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan, Saudi Arabia
- Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy
| | - Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy
| | | | - Sonali V. Mohan
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Hitendra S. Solanki
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | | | - Krishna Patel
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Shilpa Bhandi
- Department of Restorative Dental Sciences, Division of Operative Dentistry, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | - David Sidransky
- Department of Otolaryngology – Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Marco Ferrari
- Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy
- Department of Restorative Dentistry, School of Dentistry, University of Leeds, Leeds, UK
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26
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Foster JW, Shinde V, Soiberman US, Sathe G, Liu S, Wan J, Qian J, Dauoud Y, Pandey A, Jun AS, Chakravarti S. Integrated Stress Response and Decreased ECM in Cultured Stromal Cells From Keratoconus Corneas. Invest Ophthalmol Vis Sci 2019; 59:2977-2986. [PMID: 30029277 PMCID: PMC5995483 DOI: 10.1167/iovs.18-24367] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Keratoconus (KC) is a multifactorial disease where progressive thinning and weakening of the cornea leads to loss of visual acuity. Although the underlying etiology is poorly understood, a major endpoint is a dysfunctional stromal connective tissue matrix. Using multiple individual KC corneas, we determined that matrix production by keratocytes is severely impeded due to an altered stress response program. Methods KC and donor (DN) stromal keratocytes were cultured in low glucose serum-free medium containing insulin, selenium and transferrin. Fibronectin, collagens and proteins related to their chaperone, processing and export, matrix metalloproteinase, and stress response related proteins were investigated by immunoblotting, immunocytochemistry, hydroxyproline quantification, and gelatin zymography. Multiplexed mass spectrometry was used for global proteomic profiling of 5 individual DN and KC cell culture. Transcription of selected proteins was assayed by qPCR. Results DN and KC cells showed comparable survival and growth. However, immunoblotting of selected ECM proteins and global proteomics showed decreased fibronectin, collagens, PCOLCE, ADAMTS2, BMP1, HSP47, other structural and cytoskeletal proteins in KC. Phosphorylated (p) eIF2α, a translation regulator and its target, ATF4 were increased in KC cultured cells and corneal sections. Conclusions The profound decrease in structural proteins in cultured KC cells and increase in the p-eIF2α, and ATF4, suggest a stress related blockade in structural proteins not immediately needed for cell survival. Therefore, this cell culture system reveals an intrinsic aggravated stress response with consequent decrease in ECM proteins as potential pathogenic underpinnings in KC.
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Affiliation(s)
- James W Foster
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Vishal Shinde
- Department of Ophthalmology, NYU Langone Health, New York, New York, United States
| | - Uri S Soiberman
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Gajanan Sathe
- Manipal Academy of Higher Education, Karnataka, India
| | - Sheng Liu
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Julius Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Jiang Qian
- Department of Ophthalmology, NYU Langone Health, New York, New York, United States
| | - Yassine Dauoud
- Department of Ophthalmology, NYU Langone Health, New York, New York, United States
| | - Akhilesh Pandey
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Albert S Jun
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Shukti Chakravarti
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.,Department of Ophthalmology, NYU Langone Health, New York, New York, United States
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27
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Sathe G, Na CH, Renuse S, Madugundu AK, Albert M, Moghekar A, Pandey A. Quantitative Proteomic Profiling of Cerebrospinal Fluid to Identify Candidate Biomarkers for Alzheimer's Disease. Proteomics Clin Appl 2019; 13:e1800105. [PMID: 30578620 DOI: 10.1002/prca.201800105] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 12/17/2018] [Indexed: 12/13/2022]
Abstract
PURPOSE The aim of this study is to identify the potential cerebrospinal fluid (CSF) biomarkers for Alzheimer's disease and to evaluate these markers on independent CSF samples using parallel reaction monitoring (PRM) assays. EXPERIMENTAL DESIGN High-Resolution mass spectrometry and tandem mass tag (TMT) multiplexing technology are employed to identify potential biomarkers for Alzheimer's disease. Some of the identified potential biomarkers are validated using PRM assays. RESULTS A total of 2327 proteins are identified in the CSF of which 139 are observed to be significantly altered in the CSF of AD patients. The proteins altered in AD includes a number of known AD marker such as MAPT, NPTX2, VGF, GFAP, and NCAM1 as well as novel biomarkers such as PKM and YWHAG. These findings are validated in a separate set of CSF specimens from AD dementia patients and controls. NPTX2, in combination with PKM or YWHAG, leads to the best results with AUCs of 0.935 and 0.933, respectively. CONCLUSIONS AND CLINICAL RELEVANCE The proteins that are found to be altered in the CSF of patients with AD could be used for monitoring disease progression and therapeutic response and perhaps also for early detection once they are validated in larger studies.
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Affiliation(s)
- Gajanan Sathe
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India.,Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, Karnataka, India
| | - Chan Hyun Na
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Santosh Renuse
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Anil K Madugundu
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India.,Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Manipal Academy of Higher Education (MAHE), Manipal, 576104, Karnataka, India
| | - Marilyn Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Akhilesh Pandey
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, 560029, India.,Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.,Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
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28
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Sathe G, Na CH, Renuse S, Madugundu A, Albert M, Moghekar A, Pandey A. Phosphotyrosine profiling of human cerebrospinal fluid. Clin Proteomics 2018; 15:29. [PMID: 30220890 PMCID: PMC6136184 DOI: 10.1186/s12014-018-9205-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/04/2018] [Indexed: 12/21/2022] Open
Abstract
Background Cerebrospinal fluid (CSF) is an important source of potential biomarkers that affect the brain. Biomarkers for neurodegenerative disorders are needed to assist in diagnosis, monitoring disease progression and evaluating efficacy of therapies. Recent studies have demonstrated the involvement of tyrosine kinases in neuronal cell death. Thus, neurodegeneration in the brain is related to altered tyrosine phosphorylation of proteins in the brain and identification of abnormally phosphorylated tyrosine peptides in CSF has the potential to ascertain candidate biomarkers for neurodegenerative disorders. Methods In this study, we used an antibody-based tyrosine phosphopeptide enrichment method coupled with high resolution Orbitrap Fusion Tribrid Lumos Fourier transform mass spectrometer to catalog tyrosine phosphorylated peptides from cerebrospinal fluid. The subset of identified tyrosine phosphorylated peptides was also validated using parallel reaction monitoring (PRM)-based targeted approach. Results To date, there are no published studies on global profiling of phosphotyrosine modifications of CSF proteins. We carried out phosphotyrosine profiling of CSF using an anti-phosphotyrosine antibody-based enrichment and analysis using high resolution Orbitrap Fusion Lumos mass spectrometer. We identified 111 phosphotyrosine peptides mapping to 66 proteins, which included 24 proteins which have not been identified in CSF previously. We then validated a set of 5 tyrosine phosphorylated peptides in an independent set of CSF samples from cognitively normal subjects, using a PRM-based targeted approach. Conclusions The findings from this deep phosphotyrosine profiling of CSF samples have the potential to identify novel disease-related phosphotyrosine-containing peptides in CSF. Electronic supplementary material The online version of this article (10.1186/s12014-018-9205-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gajanan Sathe
- 1Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029 India.,Institute of Bioinformatics, International Technology Park, Bangalore, 560 066 India.,7Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104 India
| | - Chan Hyun Na
- 3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,4Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,6Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066 India.,3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Anil Madugundu
- 1Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029 India.,Institute of Bioinformatics, International Technology Park, Bangalore, 560 066 India.,7Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104 India
| | - Marilyn Albert
- 4Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Abhay Moghekar
- 4Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Akhilesh Pandey
- 1Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029 India.,3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,5Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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Danda R, Ganapathy K, Sathe G, Madugundu AK, Krishnan UM, Khetan V, Rishi P, Gowda H, Pandey A, Subramanian K, Prasad TSK, Elchuri SV. Membrane Proteome of Invasive Retinoblastoma: Differential Proteins and Biomarkers. Proteomics Clin Appl 2018; 12:e1700101. [DOI: 10.1002/prca.201700101] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 03/22/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Ravikanth Danda
- Department of Ocular Pathology, Vision Research Foundation; Sankara Nethralaya; Chennai 600006 Tamil Nadu India
- Centre for Nanotechnology and Advanced Biomaterials; SASTRA University; Tanjore 613401 Tamil Nadu India
| | - Kalaivani Ganapathy
- Department of Ocular Pathology, Vision Research Foundation; Sankara Nethralaya; Chennai 600006 Tamil Nadu India
| | - Gajanan Sathe
- Institute of Bioinformatics; International Technology Park; Bangalore 560066 Karnataka India
| | - Anil K. Madugundu
- Institute of Bioinformatics; International Technology Park; Bangalore 560066 Karnataka India
| | - Uma Maheswari Krishnan
- Centre for Nanotechnology and Advanced Biomaterials; SASTRA University; Tanjore 613401 Tamil Nadu India
| | - Vikas Khetan
- Shri Bhagwan Mahavir Vitreoretinal Services and Ocular Oncology Services, Medical Research Foundation; Sankara Nethralaya; Chennai 600006 Tamil Nadu India
| | - Pukhraj Rishi
- Shri Bhagwan Mahavir Vitreoretinal Services and Ocular Oncology Services, Medical Research Foundation; Sankara Nethralaya; Chennai 600006 Tamil Nadu India
| | - Harsha Gowda
- Institute of Bioinformatics; International Technology Park; Bangalore 560066 Karnataka India
- Manipal Academy of Higher Education (MAHE); Manipal 576104 Karnataka India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine; Johns Hopkins University School of Medicine; 21205 Baltimore MD USA
- Department of Pathology; Johns Hopkins University School of Medicine; 21205 Baltimore MD USA
- Department of Oncology; Johns Hopkins University School of Medicine; 21205 Baltimore MD USA
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; 21205 Baltimore MD USA
- Manipal Academy of Higher Education (MAHE); Manipal 576104 Karnataka India
| | - Krishnakumar Subramanian
- Department of Ocular Pathology, Vision Research Foundation; Sankara Nethralaya; Chennai 600006 Tamil Nadu India
| | - T. S. Keshava Prasad
- Institute of Bioinformatics; International Technology Park; Bangalore 560066 Karnataka India
| | - Sailaja V. Elchuri
- Department of Nano-Biotechnology, Vision Research Foundation; Sankara Nethralya; Chennai 600006 Tamil Nadu India
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30
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Arunima A, Yelamanchi SD, Padhi C, Jaiswal S, Ryan D, Gupta B, Sathe G, Advani J, Gowda H, Prasad TSK, Suar M. "Omics" of Food-Borne Gastroenteritis: Global Proteomic and Mutagenic Analysis of Salmonella enterica Serovar Enteritidis. OMICS 2018; 21:571-583. [PMID: 29049011 DOI: 10.1089/omi.2017.0112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Salmonella Enteritidis causes food-borne gastroenteritis by the two type three secretion systems (TTSS). TTSS-1 mediates invasion through intestinal lining, and TTSS-2 facilitates phagocytic survival. The pathogens' ability to infect effectively under TTSS-1-deficient background in host's phagocytes is poorly understood. Therefore, pathobiological understanding of TTSS-1-defective nontyphoidal Salmonellosis is highly important. We performed a comparative global proteomic analysis of the isogenic TTSS-1 mutant of Salmonella Enteritidis (M1511) and its wild-type isolate P125109. Our results showed 43 proteins were differentially expressed. Functional annotation further revealed that differentially expressed proteins belong to pathogenesis, tRNA and ncRNA metabolic processes. Three proteins, tryptophan subunit alpha chain, citrate lyase subunit alpha, and hypothetical protein 3202, were selected for in vitro analysis based on their functional annotations. Deletion mutants generated for the above proteins in the M1511 strain showed reduced intracellular survival inside macrophages in vitro. In sum, this study provides mass spectrometry-based evidence for seven hypothetical proteins, which will be subject of future investigations. Our study identifies proteins influencing virulence of Salmonella in the host. The study complements and further strengthens previously published research on proteins involved in enteropathogenesis of Salmonella and extends their role in noninvasive Salmonellosis.
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Affiliation(s)
| | - Soujanya D Yelamanchi
- 1 School of Biotechnology, KIIT University , Bhubaneswar, India .,2 Institute of Bioinformatics , International Technology Park, Bangalore, India
| | | | | | - Daniel Ryan
- 1 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Bhawna Gupta
- 1 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Gajanan Sathe
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India
| | - Jayshree Advani
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India
| | - Harsha Gowda
- 1 School of Biotechnology, KIIT University , Bhubaneswar, India .,2 Institute of Bioinformatics , International Technology Park, Bangalore, India
| | - T S Keshava Prasad
- 2 Institute of Bioinformatics , International Technology Park, Bangalore, India
| | - Mrutyunjay Suar
- 1 School of Biotechnology, KIIT University , Bhubaneswar, India
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Yelamanchi SD, Kumar M, Madugundu AK, Gopalakrishnan L, Dey G, Chavan S, Sathe G, Mathur PP, Gowda H, Mahadevan A, Shankar SK, Prasad TSK. Characterization of human pineal gland proteome. Mol Biosyst 2017; 12:3622-3632. [PMID: 27714013 DOI: 10.1039/c6mb00507a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The pineal gland is a neuroendocrine gland located at the center of the brain. It is known to regulate various physiological functions in the body through secretion of the neurohormone melatonin. Comprehensive characterization of the human pineal gland proteome has not been undertaken to date. We employed a high-resolution mass spectrometry-based approach to characterize the proteome of the human pineal gland. A total of 5874 proteins were identified from the human pineal gland in this study. Of these, 5820 proteins were identified from the human pineal gland for the first time. Interestingly, 1136 proteins from the human pineal gland were found to contain a signal peptide domain, which indicates the secretory nature of these proteins. An unbiased global proteomic profile of this biomedically important organ should benefit molecular research to unravel the role of the pineal gland in neuropsychiatric and neurodegenerative diseases.
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Affiliation(s)
- Soujanya D Yelamanchi
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and School of Biotechnology, KIIT University, Bhubaneswar 751 024, India.
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and Manipal University, Madhav Nagar, Manipal 576 104, India
| | - Anil K Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and Centre for Bioinformatics, Pondicherry University, Puducherry 605 014, India
| | | | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and Manipal University, Madhav Nagar, Manipal 576 104, India
| | - Sandip Chavan
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and Manipal University, Madhav Nagar, Manipal 576 104, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and Manipal University, Madhav Nagar, Manipal 576 104, India
| | - Premendu P Mathur
- School of Biotechnology, KIIT University, Bhubaneswar 751 024, India. and Centre for Bioinformatics, Pondicherry University, Puducherry 605 014, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and School of Biotechnology, KIIT University, Bhubaneswar 751 024, India. and YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575 018, India
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore 560 029, India. and Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore 560 029, India
| | - Susarla K Shankar
- Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore 560 029, India. and Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore 560 029, India and Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore 560 029, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575 018, India and Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore 560 029, India
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32
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Mir SA, Renuse S, Sathe G, Khan AA, Patil AH, Nanjappa V, Bhat FA, Prasad TSK, Giri AK, Chatterjee A, Gowda H. Altered signaling associated with chronic arsenic exposure in human skin keratinocytes. Proteomics Clin Appl 2017; 11. [PMID: 28731282 DOI: 10.1002/prca.201700004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 06/22/2017] [Accepted: 07/18/2017] [Indexed: 11/07/2022]
Abstract
Modulation of signaling pathways upon chronic arsenic exposure remains poorly studied. Here, we carried out SILAC-based quantitative phosphoproteomics analysis to dissect the signaling induced upon chronic arsenic exposure in human skin keratinocyte cell line, HaCaT. We identified 4171 unique phosphosites derived from 2000 proteins. We observed differential phosphorylation of 406 phosphosites (twofold) corresponding to 305 proteins. Several pathways involved in cytoskeleton maintenance and organization were found to be significantly enriched (p<0.05). Our data revealed altered phosphorylation of proteins associated with adherens junction remodeling and actin polymerization. Kinases such as protein kinase C iota type (PRKCI), mitogen-activated protein kinase kinase kinase 1 (MAP3K1), tyrosine-protein kinase BAZ1B (BAZ1B) and STE20 like kinase (SLK) were found to be hyperphosphorylated. Our study provides novel insights into signaling perturbations associated with chronic arsenic exposure in human skin keratinocytes. All MS/MS data have been deposited to the ProteomeXchange with identifier PXD004868.
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Affiliation(s)
- Sartaj Ahmad Mir
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal University, Manipal, India
| | - Santosh Renuse
- Center for Proteomics Discovery, Johns Hopkins University School of Medicine, Baltimore, MA, USA
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal University, Manipal, India
| | - Aafaque Ahmad Khan
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Arun H Patil
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | | | - Firdous Ahmad Bhat
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | - Ashok K Giri
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
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33
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Radhakrishnan A, Nanjappa V, Raja R, Sathe G, Puttamallesh VN, Jain AP, Pinto SM, Balaji SA, Chavan S, Sahasrabuddhe NA, Mathur PP, Kumar MM, Prasad TSK, Santosh V, Sukumar G, Califano JA, Rangarajan A, Sidransky D, Pandey A, Gowda H, Chatterjee A. Corrigendum: A dual specificity kinase, DYRK1A, as a potential therapeutic target for head and neck squamous cell carcinoma. Sci Rep 2017. [PMID: 28650432 PMCID: PMC5484017 DOI: 10.1038/srep46864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
This corrects the article DOI: 10.1038/srep36132.
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34
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Lu YW, Acoba MG, Selvaraju K, Huang TC, Nirujogi RS, Sathe G, Pandey A, Claypool SM. Human adenine nucleotide translocases physically and functionally interact with respirasomes. Mol Biol Cell 2017; 28:1489-1506. [PMID: 28404750 PMCID: PMC5449148 DOI: 10.1091/mbc.e17-03-0195] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 03/30/2017] [Accepted: 04/04/2017] [Indexed: 11/11/2022] Open
Abstract
A network of interactions for human adenine nucleotide translocases, required for oxidative phosphorylation, is reported. Of particular interest is an evolutionarily conserved and functionally important association with respiratory supercomplexes, which is surprising because the respirasomes of yeast and mammals are different. Members of the adenine nucleotide translocase (ANT) family exchange ADP for ATP across the mitochondrial inner membrane, an activity that is essential for oxidative phosphorylation (OXPHOS). Mutations in or dysregulation of ANTs is associated with progressive external ophthalmoplegia, cardiomyopathy, nonsyndromic intellectual disability, apoptosis, and the Warburg effect. Binding partners of human ANTs have not been systematically identified. The absence of such information has prevented a detailed molecular understanding of the assorted ANT-associated diseases, including insight into their disparate phenotypic manifestations. To fill this void, in this study, we define the interactomes of two human ANT isoforms. Analogous to its yeast counterpart, human ANTs associate with heterologous partner proteins, including the respiratory supercomplex (RSC) and other solute carriers. The evolutionarily conserved ANT–RSC association is particularly noteworthy because the composition, and thereby organization, of RSCs in yeast and human is different. Surprisingly, absence of the major ANT isoform only modestly impairs OXPHOS in HEK293 cells, indicating that the low levels of other isoforms provide functional redundancy. In contrast, pharmacological inhibition of OXPHOS expression and function inhibits ANT-dependent ADP/ATP exchange. Thus ANTs and the OXPHOS machinery physically interact and functionally cooperate to enhance ANT transport capacity and mitochondrial respiration.
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Affiliation(s)
- Ya-Wen Lu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Michelle Grace Acoba
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Kandasamy Selvaraju
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Tai-Chung Huang
- McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185.,Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University Cancer Center, Taipei 10051, Taiwan
| | - Raja S Nirujogi
- McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Gajanan Sathe
- McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Steven M Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
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35
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Radhakrishnan A, Nanjappa V, Raja R, Sathe G, Puttamallesh VN, Jain AP, Pinto SM, Balaji SA, Chavan S, Sahasrabuddhe NA, Mathur PP, Kumar MM, Prasad TSK, Santosh V, Sukumar G, Califano JA, Rangarajan A, Sidransky D, Pandey A, Gowda H, Chatterjee A. A dual specificity kinase, DYRK1A, as a potential therapeutic target for head and neck squamous cell carcinoma. Sci Rep 2016; 6:36132. [PMID: 27796319 PMCID: PMC5086852 DOI: 10.1038/srep36132] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 10/10/2016] [Indexed: 12/18/2022] Open
Abstract
Despite advances in clinical management, 5-year survival rate in patients with late-stage head and neck squamous cell carcinoma (HNSCC) has not improved significantly over the past decade. Targeted therapies have emerged as one of the most promising approaches to treat several malignancies. Though tyrosine phosphorylation accounts for a minority of total phosphorylation, it is critical for activation of signaling pathways and plays a significant role in driving cancers. To identify activated tyrosine kinase signaling pathways in HNSCC, we compared the phosphotyrosine profiles of a panel of HNSCC cell lines to a normal oral keratinocyte cell line. Dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A) was one of the kinases hyperphosphorylated at Tyr-321 in all HNSCC cell lines. Inhibition of DYRK1A resulted in an increased apoptosis and decrease in invasion and colony formation ability of HNSCC cell lines. Further, administration of the small molecular inhibitor against DYRK1A in mice bearing HNSCC xenograft tumors induced regression of tumor growth. Immunohistochemical labeling of DYRK1A in primary tumor tissues using tissue microarrays revealed strong to moderate staining of DYRK1A in 97.5% (39/40) of HNSCC tissues analyzed. Taken together our results suggest that DYRK1A could be a novel therapeutic target in HNSCC.
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Affiliation(s)
- Aneesha Radhakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India
| | - Vishalakshi Nanjappa
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Remya Raja
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Vinuth N. Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Ankit P. Jain
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- School of Biotechnology, KIIT University, Bhubaneswar 751024, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
| | - Sai A. Balaji
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Sandip Chavan
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | | | - Premendu P. Mathur
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014, India
- School of Biotechnology, KIIT University, Bhubaneswar 751024, India
| | - Mahesh M. Kumar
- Department of Neuro-Virology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India
| | - Vani Santosh
- Department of Pathology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Geethanjali Sukumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
| | - Joseph A. Califano
- Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, MD 21204, USA
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Annapoorni Rangarajan
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine,Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, 560 066, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India
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36
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Danda R, Ganapathy K, Sathe G, Madugundu AK, Ramachandran S, Krishnan UM, Khetan V, Rishi P, Keshava Prasad TS, Pandey A, Krishnakumar S, Gowda H, Elchuri SV. Proteomic profiling of retinoblastoma by high resolution mass spectrometry. Clin Proteomics 2016; 13:29. [PMID: 27799869 PMCID: PMC5080735 DOI: 10.1186/s12014-016-9128-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 09/23/2016] [Indexed: 02/07/2023] Open
Abstract
Background Retinoblastoma is an ocular neoplastic cancer caused primarily due to the mutation/deletion of RB1 gene. Due to the rarity of the disease very limited information is available on molecular changes in primary retinoblastoma. High throughput analysis of retinoblastoma transcriptome is available however the proteomic landscape of retinoblastoma remains unexplored. In the present study we used high resolution mass spectrometry-based quantitative proteomics to identify proteins associated with pathogenesis of retinoblastoma. Methods We used five pooled normal retina and five pooled retinoblastoma tissues to prepare tissue lysates. Equivalent amount of proteins from each group was trypsin digested and labeled with iTRAQ tags. The samples were analyzed on Orbitrap Velos mass spectrometer. We further validated few of the differentially expressed proteins by immunohistochemistry on primary tumors. Results We identified and quantified a total of 3587 proteins in retinoblastoma when compared with normal adult retina. In total, we identified 899 proteins that were differentially expressed in retinoblastoma with a fold change of ≥2 of which 402 proteins were upregulated and 497 were down regulated. Insulin growth factor 2 mRNA binding protein 1 (IGF2BP1), chromogranin A, fetuin A (ASHG), Rac GTPase-activating protein 1 and midkine that were found to be overexpressed in retinoblastoma were further confirmed by immunohistochemistry by staining 15 independent retinoblastoma tissue sections. We further verified the effect of IGF2BP1 on cell proliferation and migration capability of a retinoblastoma cell line using knockdown studies. Conclusions In the present study mass spectrometry-based quantitative proteomic approach was applied to identify proteins differentially expressed in retinoblastoma tumor. This study identified the mitochondrial dysfunction and lipid metabolism pathways as the major pathways to be deregulated in retinoblastoma. Further knockdown studies of IGF2BP1 in retinoblastoma cell lines revealed it as a prospective therapeutic target for retinoblastoma. Electronic supplementary material The online version of this article (doi:10.1186/s12014-016-9128-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ravikanth Danda
- Department of Ocular Pathology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu 600006 India ; Centre for Nanotechnology and Advanced Biomaterials, Shanmugha Arts, Science, Technology and Research Academy University, Tanjore, Tamilnadu India
| | - Kalaivani Ganapathy
- Department of Ocular Pathology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu 600006 India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066 India
| | - Anil K Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066 India
| | - Sharavan Ramachandran
- Department of Ocular Pathology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu 600006 India
| | - Uma Maheswari Krishnan
- Centre for Nanotechnology and Advanced Biomaterials, Shanmugha Arts, Science, Technology and Research Academy University, Tanjore, Tamilnadu India
| | - Vikas Khetan
- Shri Bhagwan Mahavir Vitreoretinal Services and Ocular Oncology Services, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu 600006 India
| | - Pukhraj Rishi
- Shri Bhagwan Mahavir Vitreoretinal Services and Ocular Oncology Services, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu 600006 India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066 India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Subramanian Krishnakumar
- Department of Ocular Pathology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu 600006 India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560066 India
| | - Sailaja V Elchuri
- Department of Nano-Biotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu 600006 India
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Sathe G, Pinto SM, Syed N, Nanjappa V, Solanki HS, Renuse S, Chavan S, Khan AA, Patil AH, Nirujogi RS, Nair B, Mathur PP, Prasad TSK, Gowda H, Chatterjee A. Phosphotyrosine profiling of curcumin-induced signaling. Clin Proteomics 2016; 13:13. [PMID: 27307780 PMCID: PMC4908701 DOI: 10.1186/s12014-016-9114-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 05/04/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Curcumin, derived from the rhizome Curcuma longa, is a natural anti-cancer agent and has been shown to inhibit proliferation and survival of tumor cells. Although the anti-cancer effects of curcumin are well established, detailed understanding of the signaling pathways altered by curcumin is still lacking. In this study, we carried out SILAC-based quantitative proteomic analysis of a HNSCC cell line (CAL 27) to investigate tyrosine signaling in response to curcumin. RESULTS Using high resolution Orbitrap Fusion Tribrid Fourier transform mass spectrometer, we identified 627 phosphotyrosine sites mapping to 359 proteins. We observed alterations in the level of phosphorylation of 304 sites corresponding to 197 proteins upon curcumin treatment. We report here for the first time, curcumin-induced alterations in the phosphorylation of several kinases including TNK2, FRK, AXL, MAPK12 and phosphatases such as PTPN6, PTPRK, and INPPL1 among others. Pathway analysis revealed that the proteins differentially phosphorylated in response to curcumin are known to be involved in focal adhesion kinase signaling and actin cytoskeleton reorganization. CONCLUSIONS The study indicates that curcumin may regulate cellular processes such as proliferation and migration through perturbation of the focal adhesion kinase pathway. This is the first quantitative phosphoproteomics-based study demonstrating the signaling events that are altered in response to curcumin. Considering the importance of curcumin as an anti-cancer agent, this study will significantly improve the current knowledge of curcumin-mediated signaling in cancer.
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Affiliation(s)
- Gajanan Sathe
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,Manipal University, Madhav Nagar, Manipal, 576104 India
| | - Sneha M Pinto
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018 India
| | - Nazia Syed
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry, 605014 India
| | - Vishalakshi Nanjappa
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,Amrita School of Biotechnology, Amrita University, Kollam, 690525 India
| | - Hitendra S Solanki
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,School of Biotechnology, KIIT University, Bhubaneswar, 751024 India
| | - Santosh Renuse
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,Amrita School of Biotechnology, Amrita University, Kollam, 690525 India
| | - Sandip Chavan
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,Manipal University, Madhav Nagar, Manipal, 576104 India
| | - Aafaque Ahmad Khan
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,School of Biotechnology, KIIT University, Bhubaneswar, 751024 India
| | - Arun H Patil
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,School of Biotechnology, KIIT University, Bhubaneswar, 751024 India
| | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, 605014 India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita University, Kollam, 690525 India
| | | | - T S Keshava Prasad
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018 India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, 560029 India
| | - Harsha Gowda
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018 India
| | - Aditi Chatterjee
- Institute of Bioinformatics, Unit I, 7th Floor, Discoverer Building, International Tech Park, Bangalore, 560066 India.,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018 India
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Bhattacharjee M, Balakrishnan L, Renuse S, Advani J, Goel R, Sathe G, Keshava Prasad TS, Nair B, Jois R, Shankar S, Pandey A. Synovial fluid proteome in rheumatoid arthritis. Clin Proteomics 2016; 13:12. [PMID: 27274716 PMCID: PMC4893419 DOI: 10.1186/s12014-016-9113-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/26/2016] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) is a chronic autoinflammatory disorder that affects small joints. Despite intense efforts, there are currently no definitive markers for early diagnosis of RA and for monitoring the progression of this disease, though some of the markers like anti CCP antibodies and anti vimentin antibodies are promising. We sought to catalogue the proteins present in the synovial fluid of patients with RA. It was done with the aim of identifying newer biomarkers, if any, that might prove promising in future. METHODS To enrich the low abundance proteins, we undertook two approaches-multiple affinity removal system (MARS14) to deplete some of the most abundant proteins and lectin affinity chromatography for enrichment of glycoproteins. The peptides were analyzed by LC-MS/MS on a high resolution Fourier transform mass spectrometer. RESULTS This effort was the first total profiling of the synovial fluid proteome in RA that led to identification of 956 proteins. From the list, we identified a number of functionally significant proteins including vascular cell adhesion molecule-1, S100 proteins, AXL receptor protein tyrosine kinase, macrophage colony stimulating factor (M-CSF), programmed cell death ligand 2 (PDCD1LG2), TNF receptor 2, (TNFRSF1B) and many novel proteins including hyaluronan-binding protein 2, semaphorin 4A (SEMA4D) and osteoclast stimulating factor 1. Overall, our findings illustrate the complex and dynamic nature of RA in which multiple pathways seems to be participating actively. CONCLUSIONS The use of high resolution mass spectrometry thus, enabled identification of proteins which might be critical to the progression of RA.
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Affiliation(s)
- Mitali Bhattacharjee
- />Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
- />Amrita School of Biotechnology, Amrita University, Kollam, 690525 India
| | - Lavanya Balakrishnan
- />Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
- />Department of Biotechnology, Kuvempu University, Shankaraghatta, 577451 India
| | - Santosh Renuse
- />Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
- />Amrita School of Biotechnology, Amrita University, Kollam, 690525 India
| | - Jayshree Advani
- />Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
- />Manipal University, Madhav Nagar, Manipal, 576104 India
| | - Renu Goel
- />Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
- />Department of Biotechnology, Kuvempu University, Shankaraghatta, 577451 India
| | - Gajanan Sathe
- />Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
- />Manipal University, Madhav Nagar, Manipal, 576104 India
| | - T. S. Keshava Prasad
- />Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
- />Amrita School of Biotechnology, Amrita University, Kollam, 690525 India
| | - Bipin Nair
- />Amrita School of Biotechnology, Amrita University, Kollam, 690525 India
| | - Ramesh Jois
- />Department of Rheumatology, Fortis Hospital, Bangalore, 560066 India
| | - Subramanian Shankar
- />Department of Rheumatology, Medical Division, Command Hospital (Air Force), Bangalore, 560007 India
| | - Akhilesh Pandey
- />McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, BRB 527, Baltimore, MD 21205 USA
- />Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- />Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- />Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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Radhakrishnan A, Nanjappa V, Raja R, Sathe G, Chavan S, Nirujogi RS, Patil AH, Solanki H, Renuse S, Sahasrabuddhe NA, Mathur PP, Prasad TSK, Kumar P, Califano JA, Sidransky D, Pandey A, Gowda H, Chatterjee A. Dysregulation of splicing proteins in head and neck squamous cell carcinoma. Cancer Biol Ther 2016; 17:219-29. [PMID: 26853621 DOI: 10.1080/15384047.2016.1139234] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Signaling plays an important role in regulating all cellular pathways. Altered signaling is one of the hallmarks of cancers. Phosphoproteomics enables interrogation of kinase mediated signaling pathways in biological systems. In cancers, this approach can be utilized to identify aberrantly activated pathways that potentially drive proliferation and tumorigenesis. To identify signaling alterations in head and neck squamous cell carcinoma (HNSCC), we carried out proteomic and phosphoproteomic analysis of HNSCC cell lines using a combination of tandem mass tag (TMT) labeling approach and titanium dioxide-based enrichment. We identified 4,920 phosphosites corresponding to 2,212 proteins in six HNSCC cell lines compared to a normal oral cell line. Our data indicated significant enrichment of proteins associated with splicing. We observed hyperphosphorylation of SRSF protein kinase 2 (SRPK2) and its downstream substrates in HNSCC cell lines. SRPK2 is a splicing kinase, known to phosphorylate serine/arginine (SR) rich domain proteins and regulate splicing process in eukaryotes. Although genome-wide studies have reported the contribution of alternative splicing events of several genes in the progression of cancer, the involvement of splicing kinases in HNSCC is not known. In this study, we studied the role of SRPK2 in HNSCC. Inhibition of SRPK2 resulted in significant decrease in colony forming and invasive ability in a panel of HNSCC cell lines. Our results indicate that phosphorylation of SRPK2 plays a crucial role in the regulation of splicing process in HNSCC and that splicing kinases can be developed as a new class of therapeutic target in HNSCC.
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Affiliation(s)
- Aneesha Radhakrishnan
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,b Department of Biochemistry and Molecular Biology , Pondicherry University , Puducherry , India
| | - Vishalakshi Nanjappa
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,c Amrita School of Biotechnology, Amrita University , Kollam , India
| | - Remya Raja
- a Institute of Bioinformatics, International Technology Park , Bangalore , India
| | - Gajanan Sathe
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,d Manipal University , Madhav Nagar, Manipal , India
| | - Sandip Chavan
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,d Manipal University , Madhav Nagar, Manipal , India
| | - Raja Sekhar Nirujogi
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,e Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry , India
| | - Arun H Patil
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,f School of Biotechnology, KIIT University , Bhubaneswar , India
| | - Hitendra Solanki
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,f School of Biotechnology, KIIT University , Bhubaneswar , India
| | - Santosh Renuse
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,c Amrita School of Biotechnology, Amrita University , Kollam , India
| | | | - Premendu P Mathur
- b Department of Biochemistry and Molecular Biology , Pondicherry University , Puducherry , India.,f School of Biotechnology, KIIT University , Bhubaneswar , India
| | - T S Keshava Prasad
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,c Amrita School of Biotechnology, Amrita University , Kollam , India.,e Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry , India.,g YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore , India
| | - Prashant Kumar
- a Institute of Bioinformatics, International Technology Park , Bangalore , India
| | - Joseph A Califano
- h Milton J Dance Head and Neck Center, Greater Baltimore Medical Center , Baltimore , MD , USA.,i Department of Otolaryngology-Head and Neck Surgery , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - David Sidransky
- i Department of Otolaryngology-Head and Neck Surgery , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Akhilesh Pandey
- j McKusick-Nathans Institute of Genetic Medicine , Baltimore , MD , USA.,k Departments of Biological Chemistry , Baltimore , MD , USA.,l Oncology and Pathology, Johns Hopkins University School of Medicine , Baltimore , MD , USA.,m Pathology, Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Harsha Gowda
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,g YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore , India
| | - Aditi Chatterjee
- a Institute of Bioinformatics, International Technology Park , Bangalore , India.,g YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore , India
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40
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Jamdhade MD, Pawar H, Chavan S, Sathe G, Umasankar PK, Mahale KN, Dixit T, Madugundu AK, Prasad TSK, Gowda H, Pandey A, Patole MS. Comprehensive proteomics analysis of glycosomes from Leishmania donovani. OMICS 2015; 19:157-70. [PMID: 25748437 DOI: 10.1089/omi.2014.0163] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Leishmania donovani is a kinetoplastid protozoan that causes a severe and fatal disease kala-azar, or visceral leishmaniasis. L. donovani infects human host after the phlebotomine sandfly takes a blood meal and resides within the phagolysosome of infected macrophages. Previous studies on host-parasite interactions have not focused on Leishmania organelles and the role that they play in the survival of this parasite within macrophages. Leishmania possess glycosomes that are unique and specialized subcellular microbody organelles. Glycosomes are known to harbor most peroxisomal enzymes and, in addition, they also possess nine glycolytic enzymes. In the present study, we have carried out proteomic profiling using high resolution mass spectrometry of a sucrose density gradient-enriched glycosomal fraction isolated from L. donovani promastigotes. This study resulted in the identification of 4022 unique peptides, leading to the identification of 1355 unique proteins from a preparation enriched in L. donovani glycosomes. Based on protein annotation, 566 (41.8%) were identified as hypothetical proteins with no known function. A majority of the identified proteins are involved in metabolic processes such as carbohydrate, lipid, and nucleic acid metabolism. Our present proteomic analysis is the most comprehensive study to date to map the proteome of L. donovani glycosomes.
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41
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Subbannayya T, Leal-Rojas P, Barbhuiya MA, Raja R, Renuse S, Sathe G, Pinto SM, Syed N, Nanjappa V, Patil AH, Garcia P, Sahasrabuddhe NA, Nair B, Guerrero-Preston R, Navani S, Tiwari PK, Santosh V, Sidransky D, Prasad TSK, Gowda H, Roa JC, Pandey A, Chatterjee A. Macrophage migration inhibitory factor - a therapeutic target in gallbladder cancer. BMC Cancer 2015; 15:843. [PMID: 26530123 PMCID: PMC4632274 DOI: 10.1186/s12885-015-1855-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 10/27/2015] [Indexed: 12/20/2022] Open
Abstract
Background Poor prognosis in gallbladder cancer is due to late presentation of the disease, lack of reliable biomarkers for early diagnosis and limited targeted therapies. Early diagnostic markers and novel therapeutic targets can significantly improve clinical management of gallbladder cancer. Methods Proteomic analysis of four gallbladder cancer cell lines based on the invasive property (non-invasive to highly invasive) was carried out using the isobaric tags for relative and absolute quantitation labeling-based quantitative proteomic approach. The expression of macrophage migration inhibitory factor was analysed in gallbladder adenocarcinoma tissues using immunohistochemistry. In vitro cellular assays were carried out in a panel of gallbladder cancer cell lines using MIF inhibitors, ISO-1 and 4-IPP or its specific siRNA. Results The quantitative proteomic experiment led to the identification of 3,653 proteins, among which 654 were found to be overexpressed and 387 were downregulated in the invasive cell lines (OCUG-1, NOZ and GB-d1) compared to the non-invasive cell line, TGBC24TKB. Among these, macrophage migration inhibitory factor (MIF) was observed to be highly overexpressed in two of the invasive cell lines. MIF is a pleiotropic proinflammatory cytokine that plays a causative role in multiple diseases, including cancer. MIF has been reported to play a central role in tumor cell proliferation and invasion in several cancers. Immunohistochemical labeling of tumor tissue microarrays for MIF expression revealed that it was overexpressed in 21 of 29 gallbladder adenocarcinoma cases. Silencing/inhibition of MIF using siRNA and/or MIF antagonists resulted in a significant decrease in cell viability, colony forming ability and invasive property of the gallbladder cancer cells. Conclusions Our findings support the role of MIF in tumor aggressiveness and suggest its potential application as a therapeutic target for gallbladder cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1855-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tejaswini Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,Amrita School of Biotechnology, Amrita University, Kollam, 690525, India.
| | - Pamela Leal-Rojas
- Department of Pathology, Center of Genetic and Immunological Studies (CEGIN) and Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile. .,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Mustafa A Barbhuiya
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Adrienne Helis Malvin Research Foundation, New Orleans, LA, 70130, USA.
| | - Remya Raja
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,Amrita School of Biotechnology, Amrita University, Kollam, 690525, India.
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,Manipal University, Madhav Nagar, Manipal, 576104, India.
| | - Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018, India.
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
| | - Vishalakshi Nanjappa
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,Amrita School of Biotechnology, Amrita University, Kollam, 690525, India.
| | - Arun H Patil
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India.
| | - Patricia Garcia
- Department of Pathology, Advanced Center for Chronic Diseases (ACCDiS), CITO, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | | | - Bipin Nair
- Amrita School of Biotechnology, Amrita University, Kollam, 690525, India.
| | - Rafael Guerrero-Preston
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
| | | | - Pramod K Tiwari
- Centre for Genomics, Molecular and Human Genetics, Jiwaji University, Gwalior, 474011, India. .,School of Studies in Zoology, Jiwaji University, Gwalior, India.
| | - Vani Santosh
- Department of Pathology, National Institute of Mental Health and Neurosciences, Bangalore, 560029, India.
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,Amrita School of Biotechnology, Amrita University, Kollam, 690525, India. .,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018, India. .,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, 560029, India.
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018, India.
| | - Juan Carlos Roa
- Department of Pathology, Advanced Center for Chronic Diseases (ACCDiS), CITO, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Departments of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India. .,Manipal University, Madhav Nagar, Manipal, 576104, India. .,YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018, India.
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Syed N, Chavan S, Sahasrabuddhe NA, Renuse S, Sathe G, Nanjappa V, Radhakrishnan A, Raja R, Pinto SM, Srinivasan A, Prasad TSK, Srikumar K, Gowda H, Santosh V, Sidransky D, Califano JA, Pandey A, Chatterjee A. Silencing of high-mobility group box 2 (HMGB2) modulates cisplatin and 5-fluorouracil sensitivity in head and neck squamous cell carcinoma. Proteomics 2015; 15:383-93. [PMID: 25327479 DOI: 10.1002/pmic.201400338] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/24/2014] [Accepted: 10/13/2014] [Indexed: 12/16/2022]
Abstract
Dysregulation of protein expression is associated with most diseases including cancer. MS-based proteomic analysis is widely employed as a tool to study protein dysregulation in cancers. Proteins that are differentially expressed in head and neck squamous cell carcinoma (HNSCC) cell lines compared to the normal oral cell line could serve as biomarkers for patient stratification. To understand the proteomic complexity in HNSCC, we carried out iTRAQ-based MS analysis on a panel of HNSCC cell lines in addition to a normal oral keratinocyte cell line. LC-MS/MS analysis of total proteome of the HNSCC cell lines led to the identification of 3263 proteins, of which 185 proteins were overexpressed and 190 proteins were downregulated more than twofold in at least two of the three HNSCC cell lines studied. Among the overexpressed proteins, 23 proteins were related to DNA replication and repair. These included high-mobility group box 2 (HMGB2) protein, which was overexpressed in all three HNSCC lines studied. Overexpression of HMGB2 has been reported in various cancers, yet its role in HNSCC remains unclear. Immunohistochemical labeling of HMGB2 in a panel of HNSCC tumors using tissue microarrays revealed overexpression in 77% (54 of 70) of tumors. The HMGB proteins are known to bind to DNA structure resulting from cisplatin-DNA adducts and affect the chemosensitivity of cells. We observed that siRNA-mediated silencing of HMGB2 increased the sensitivity of the HNSCC cell lines to cisplatin and 5-FU. We hypothesize that targeting HMGB2 could enhance the efficacy of existing chemotherapeutic regimens for treatment of HNSCC. All MS data have been deposited in the ProteomeXchange with identifier PXD000737 (http://proteomecentral.proteomexchange.org/dataset/PXD000737).
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Affiliation(s)
- Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, India; Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry, India
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Pawar H, Srikanth SM, Kashyap MK, Sathe G, Chavan S, Singal M, Manju HC, Kumar KVV, Vijayakumar M, Sirdeshmukh R, Pandey A, Prasad TSK, Gowda H, Kumar RV. Downregulation of S100 Calcium Binding Protein A9 in Esophageal Squamous Cell Carcinoma. ScientificWorldJournal 2015; 2015:325721. [PMID: 26788548 PMCID: PMC4691646 DOI: 10.1155/2015/325721] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 11/16/2015] [Indexed: 02/07/2023] Open
Abstract
The development of esophageal squamous cell carcinoma (ESCC) is poorly understood and the major regulatory molecules involved in the process of tumorigenesis have not yet been identified. We had previously employed a quantitative proteomic approach to identify differentially expressed proteins in ESCC tumors. A total of 238 differentially expressed proteins were identified in that study including S100 calcium binding protein A9 (S100A9) as one of the major downregulated proteins. In the present study, we carried out immunohistochemical validation of S100A9 in a large cohort of ESCC patients to determine the expression and subcellular localization of S100A9 in tumors and adjacent normal esophageal epithelia. Downregulation of S100A9 was observed in 67% (n = 192) of 288 different ESCC tumors, with the most dramatic downregulation observed in the poorly differentiated tumors (99/111). Expression of S100A9 was restricted to the prickle and functional layers of normal esophageal mucosa and localized predominantly in the cytoplasm and nucleus whereas virtually no expression was observed in the tumor and stromal cells. This suggests the important role that S100A9 plays in maintaining the differentiated state of epithelium and suggests that its downregulation may be associated with increased susceptibility to tumor formation.
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Affiliation(s)
- Harsh Pawar
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- 2Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
- 3Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore 560029, India
- 4Department of Zoology, Savitribai Phule Pune University, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Srinivas M. Srikanth
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- 5Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 605014, India
| | - Manoj Kumar Kashyap
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- 6McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- 7Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- 8Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0960, USA
| | - Gajanan Sathe
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Sandip Chavan
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Mukul Singal
- 9Government Medical College and Hospital, Sector 32, Chandigarh 160030, India
| | - H. C. Manju
- 3Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore 560029, India
| | | | - M. Vijayakumar
- 10Department of Surgical Oncology, Kidwai Memorial Institute of Oncology, Bangalore 560029, India
| | - Ravi Sirdeshmukh
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Akhilesh Pandey
- 6McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- 7Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- 11Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- 12Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - T. S. Keshava Prasad
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- 5Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 605014, India
| | - Harsha Gowda
- 1Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- *Harsha Gowda: and
| | - Rekha V. Kumar
- 3Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore 560029, India
- *Rekha V. Kumar:
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Pawar H, Renuse S, Khobragade SN, Chavan S, Sathe G, Kumar P, Mahale KN, Gore K, Kulkarni A, Dixit T, Raju R, Prasad TSK, Harsha HC, Patole MS, Pandey A. Neglected Tropical Diseases and Omics Science: Proteogenomics Analysis of the Promastigote Stage ofLeishmania majorParasite. OMICS: A Journal of Integrative Biology 2014; 18:499-512. [DOI: 10.1089/omi.2013.0159] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Harsh Pawar
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Rajiv Gandhi University of Health Sciences, Bangalore, India
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Department of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | | | - Sandip Chavan
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal University, Madhav Nagar, Manipal, India
| | - Praveen Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | | | | | | | - Tanwi Dixit
- National Centre for Cell Sciences, Pune, India
| | - Rajesh Raju
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | | | - H. C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | | | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Nirujogi RS, Pawar H, Renuse S, Kumar P, Chavan S, Sathe G, Sharma J, Khobragade S, Pande J, Modak B, Prasad TSK, Harsha HC, Patole MS, Pandey A. Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani. J Proteomics 2013; 97:48-61. [PMID: 23665000 DOI: 10.1016/j.jprot.2013.04.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 04/02/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
Abstract
UNLABELLED The kinetoplastid protozoan parasite, Leishmania donovani, is the causative agent of kala azar or visceral leishmaniasis. Kala azar is a severe form of leishmaniasis that is fatal in the majority of untreated cases. Studies on proteomic analysis of L. donovani thus far have been carried out using homology-based identification based on related Leishmania species (L. infantum, L. major and L. braziliensis) whose genomes have been sequenced. Recently, the genome of L. donovani was fully sequenced and the data became publicly available. We took advantage of the availability of its genomic sequence to carry out a more accurate proteogenomic analysis of L. donovani proteome using our previously generated dataset. This resulted in identification of 17,504 unique peptides upon database-dependent search against the annotated proteins in L. donovani. These peptides were assigned to 3999 unique proteins in L. donovani. 2296 proteins were identified in both the life stages of L. donovani, while 613 and 1090 proteins were identified only from amastigote and promastigote stages, respectively. The proteomic data was also searched against six-frame translated L. donovani genome, which led to 255 genome search-specific peptides (GSSPs) resulting in identification of 20 novel genes and correction of 40 existing gene models in L. donovani. BIOLOGICAL SIGNIFICANCE Leishmania donovani genome sequencing was recently completed, which permitted us to use a proteogenomic approach to map its proteome and to carry out annotation of it genome. This resulted in mapping of 50% (3999 proteins) of L. donovani proteome. Our study identified 20 novel genes previously not predicted from the L. donovani genome in addition to correcting annotations of 40 existing gene models. The identified proteins may help in better understanding of stage-specific protein expression profiles in L. donovani and to identify novel stage-specific drug targets in L. donovani which could be used in the treatment of leishmaniasis. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Harsh Pawar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Rajiv Gandhi University of Health Sciences, Bangalore 560041, India
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Department of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Praveen Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Sandip Chavan
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Manipal University, Madhav Nagar, Manipal 576104, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Manipal University, Madhav Nagar, Manipal 576104, India
| | - Jyoti Sharma
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Manipal University, Madhav Nagar, Manipal 576104, India
| | | | | | - Bhakti Modak
- National Centre for Cell Sciences, Pune 411007, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605014, India; Manipal University, Madhav Nagar, Manipal 576104, India
| | - H C Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | | | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA.
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Pawar H, Maharudraiah J, Kashyap MK, Sharma J, Srikanth SM, Choudhary R, Chavan S, Sathe G, Manju HC, Kumar KVV, Vijayakumar M, Sirdeshmukh R, Harsha HC, Prasad TSK, Pandey A, Kumar RV. Downregulation of cornulin in esophageal squamous cell carcinoma. Acta Histochem 2013; 115:89-99. [PMID: 22560086 DOI: 10.1016/j.acthis.2012.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 04/04/2012] [Accepted: 04/15/2012] [Indexed: 02/07/2023]
Abstract
Early events in the development of esophageal squamous cell carcinoma (ESCC) are poorly understood and many of the key molecules involved have not yet been identified. We previously used isobaric tags for a relative and absolute quantitation (iTRAQ)-based quantitative proteomics approach to identify differentially expressed proteins in ESCC tissue as compared to the adjacent normal mucosa. Cornulin was identified as one of the major downregulated molecules in ESCC. Cornulin is a member of the S100 fused-type protein family, which has an EF-hand calcium binding motif and multiple tandem repeats of specific peptide motifs. Cornulin was 5-fold downregulated in ESCC as compared to normal epithelium mirroring our previous findings in a gene expression study of ESCC. In the present study, we performed immunohistochemical validation of cornulin (CRNN) in a larger set of patients with ESCC. Downregulation of cornulin was observed in 89% (n=239) of 266 different ESCC tissues arrayed on tissue microarrays (TMAs). Expression of cornulin was observed in the prickle and functional cell layers of normal esophageal mucosa, localized predominantly in the cytoplasm and perinuclear region. The large majority of ESCC cases had little or no expression of cornulin in the carcinoma or stroma. These findings suggest that cornulin is an important molecule in normal esophageal pathology and is likely lost during the conversion of normal to neoplastic epithelium.
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Affiliation(s)
- Harsh Pawar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
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Connor JR, Kumar S, Sathe G, Mooney J, O'Brien SP, Mui P, Murdock PR, Gowen M, Lark MW. Clusterin expression in adult human normal and osteoarthritic articular cartilage. Osteoarthritis Cartilage 2001; 9:727-37. [PMID: 11795992 DOI: 10.1053/joca.2001.0475] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To characterize the expression pattern of clusterin in adult human normal and osteoarthritic cartilage. METHODS Clusterin mRNA expression in adult human normal and osteoarthritic cartilage was investigated by analysis of cDNA libraries, TaqMan quantitative RT-PCR, microarray and in situ hybridization. RESULTS Sequence analysis of ESTs from adult human normal and osteoarthritic cartilage cDNA libraries demonstrated that the abundance of clusterin in these libraries was equivalent to genes which have been more commonly associated with cartilage. To examine tissue distribution, TaqMan Quantitative PCR analysis was performed using RNA from a panel of individual normal tissues. Clusterin was expressed at significant levels in cartilage, brain, liver, and pancreas. The expression of clusterin mRNA was up-regulated in early osteoarthritic vs normal cartilage when analysed by microarray analysis. Using in situ hybridization, chondrocytes of normal cartilage expressed moderate levels of clusterin. Upper mid-zone chondrocytes in cartilage with early stages of osteoarthritic disease expressed high levels of clusterin mRNA. In advanced osteoarthritic cartilage, the overall expression of clusterin was reduced. CONCLUSION The induction of clusterin has been associated with a variety of disease states where it appears to provide a cytoprotective effect. The increased expression of clusterin mRNA in the early stages of osteoarthritis (OA) may reflect an attempt by the chondrocytes to protect and repair the tissue. In contrast, the decrease in clusterin mRNA in the advanced osteoarthritic cartilage accompanies the final degenerative stages of the disease. An understanding of the expression of clusterin in osteoarthritis may allow consideration of this protein as a marker for cartilage changes in this chronic degenerative condition.
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Affiliation(s)
- J R Connor
- Department of Musculoskeletal Diseases, GlaxoSmithKline Pharmaceuticals, King of Prussia, Pennsylvania 19406, USA.
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Kumar S, Connor JR, Dodds RA, Halsey W, Van Horn M, Mao J, Sathe G, Mui P, Agarwal P, Badger AM, Lee JC, Gowen M, Lark MW. Identification and initial characterization of 5000 expressed sequenced tags (ESTs) each from adult human normal and osteoarthritic cartilage cDNA libraries. Osteoarthritis Cartilage 2001; 9:641-53. [PMID: 11597177 DOI: 10.1053/joca.2001.0421] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To prepare, sequence and analyse adult human cartilage cDNA libraries to study the gene expression pattern between normal and osteoarthritic cartilage. METHODS Poly A(+)RNA from adult human normal and osteoarthritic articular cartilage was isolated and used to prepare cDNA libraries. Approximately 5000 ESTs from each library were sequenced and analysed using bioinformatic tools. The expression of select genes was confirmed by Northern blot and in situ hybridization analysis. RESULTS Multiple gene families including several classical cartilage matrix protein encoding genes were identified. Approximately 28-40% of the genes sequenced from these libraries were novel, while half of the genes encoded known proteins and 4-6% of the genes encoded novel homologs of known proteins. Several known genes, whose expression has not been reported previously in cartilage, were also identified. We have confirmed the cartilage expression of three known (CTGF, CTGF-L and clusterin) and two novel homologs of known genes (PCPE-2 and Gal-Nac transferase) by Northern blot and in situ hybridization analysis. CONCLUSION This is the first report of the preparation and sequencing of cDNA libraries from adult human normal and osteoarthritic articular cartilage. Further analysis of genes identified from these libraries may provide molecular targets for diagnosis and/or treatment of osteoarthritis (OA).
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Affiliation(s)
- S Kumar
- Department of Musculoskeletal Diseases, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Rd, King of Prussia, Pennsylvania 19406, USA.
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Hu E, Chen Z, Fredrickson T, Gellai M, Jugus M, Contino L, Spurr N, Sims M, Halsey W, Van Horn S, Mao J, Sathe G, Brooks D. Identification of a novel kidney-specific gene downregulated in acute ischemic renal failure. Am J Physiol Renal Physiol 2000; 279:F426-39. [PMID: 10966922 DOI: 10.1152/ajprenal.2000.279.3.f426] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
To gain further insights into the molecular mechanisms involved in acute renal failure, we have isolated a new gene from rat and human, named KSP32 (kidney-specific protein with a molecular mass of 32 kDa). KSP32 encodes a novel gene that shows little homology to other mammalian proteins. It, however, shares extensive homology with several proteins found in the nematode Caenorhabditis elegans and plants. The expression of KSP32 mRNA is highly restricted to kidney. In situ hybidization analysis revealed that the expression of KSP32 mRNA was prominent in the boundary of kidney cortex and outer medulla, exhibiting a raylike formation extending from the medulla into the cortex. Finally, KSP32 mRNA was dramatically downregulated in rat following induction of acute ischemic renal failure. Rapid loss of KSP32 mRNA expression was observed beginning at approximately 5 h following renal injury and mRNA levels remained depressed for at least 96 h. Both KSP32 mRNA levels as well as renal function recovered 14 days after injury. Administration of an endothelin receptor antagonist (SB-209670), known to restore renal function, significantly increased KSP32 expression.
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Affiliation(s)
- E Hu
- Department of Renal Pharmacology, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19403, USA.
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Sarau HM, Ames RS, Chambers J, Ellis C, Elshourbagy N, Foley JJ, Schmidt DB, Muccitelli RM, Jenkins O, Murdock PR, Herrity NC, Halsey W, Sathe G, Muir AI, Nuthulaganti P, Dytko GM, Buckley PT, Wilson S, Bergsma DJ, Hay DW. Identification, molecular cloning, expression, and characterization of a cysteinyl leukotriene receptor. Mol Pharmacol 1999; 56:657-63. [PMID: 10462554 DOI: 10.1124/mol.56.3.657] [Citation(s) in RCA: 272] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The cysteinyl leukotrienes (CysLTs) have been implicated in the pathophysiology of inflammatory disorders, in particular asthma, for which the CysLT receptor antagonists pranlukast, zafirlukast, and montelukast, have been introduced recently as novel therapeutics. Here we report on the molecular cloning, expression, localization, and pharmacological characterization of a CysLT receptor (CysLTR), which was identified by ligand fishing of orphan seven-transmembrane-spanning, G protein-coupled receptors. This receptor, expressed in human embryonic kidney (HEK)-293 cells responded selectively to the individual CysLTs, LTC(4), LTD(4), or LTE(4), with a calcium mobilization response; the rank order potency was LTD(4) (EC(50) = 2.5 nM) > LTC(4) (EC(50) = 24 nM) > LTE(4) (EC(50) = 240 nM). Evidence was provided that LTE(4) is a partial agonist at this receptor. [(3)H]LTD(4) binding and LTD(4)-induced calcium mobilization in HEK-293 cells expressing the CysLT receptor were potently inhibited by the structurally distinct CysLTR antagonists pranlukast, montelukast, zafirlukast, and pobilukast; the rank order potency was pranlukast = zafirlukast > montelukast > pobilukast. LTD(4)-induced calcium mobilization in HEK-293 cells expressing the CysLT receptor was not affected by pertussis toxin, and the signal appears to be the result of the release from intracellular stores. Localization studies indicate the expression of this receptor in several tissues, including human lung, human bronchus, and human peripheral blood leukocytes. The discovery of this receptor, which has characteristics of the purported CysLT(1) receptor subtype, should assist in the elucidation of the pathophysiological roles of the CysLTs and in the identification of additional receptor subtypes.
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Affiliation(s)
- H M Sarau
- Department of Pulmonary Pharmacology, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania, USA
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